So the short answer is that there is not such a model structure. The difficulty arises in trying to show that the class of weak equivalences has all of the necessary properties; in particular, even two-of-three does not hold for the naive definition. The first difficulty arises even before that: on ordinary simplicial sets we can arrange for a model of every set that is "minimal" on the $\pi_0$-level, meaning that every connected component has exactly one $0$-simplex. In simplicial commutative monoids we can no longer do this. However, we could assume that in order to be a weak equivalence we need to be a $\pi_*$-isomorphism when choosing any (coherently chosen) basepoints.
For the purposes of our discussion we are going to assume that $\pi_*$-equivalences use the model $S^n = \Delta^n/\partial\Delta^n$. (This is the model that most closely mimicks the boundary maps in the Dold-Kan correspondence.) Now let $X = S^2$, and let $Y$ be $S^2$ with an extra $0$-simplex connected by a $1$-simplex to the original basepoint. (So it looks like a balloon on a string.) We define a map $X\rightarrow Y$ to be the inclusion of $S^2$ in the obvious manner, and a map $Y\rightarrow X$ to be collapsing the extra $1$-simplex back down. Then the composition of these two maps is the identity on $X$, so obviously a weak equivalence. The map $X\rightarrow Y$ is also a weak equivalence, because adding the "string" can't add any new homotopy groups to $X$. However, the map $Y\rightarrow X$ is not a weak equivalence, as $\pi_2Y$ based at the extra point is a one-point set but $\pi_2X$ at its image is a two-point set.
The problem arose because in order to show that $\pi_*$ was invariant of basepoint in the usual Kan complex model we needed to be able to "pull back" simplices along paths in the simplicial set, which used the Kan condition. The new model does not have such a condition, and thus we can't necessarily pull things back.
Another observation along these lines. Take any connected simplicial set $X$, and let $Y$ be $X$ with a "string" added to it at any basepoint. Then $*\rightarrow Y$ (including into the new point) is a weak equivalence, and $X\rightarrow Y$ (including into itself) is a weak equivalence. Thus in the homotopy category, $X$ is isomorphic to a point (and thus the homotopy category is just the category of sets) ... which is presumably not desired.
-- The Bourbon seminar
I am not knowledgeable enough to have much to say I have not writen in my answer to a previous question of yours, and I think that David Roberts's answer (or, rather immodestly, my previous one) provides what you were looking for as regards your first question. Just a few additional small points:
Pursuing Stacks is not a letter. See Tim Porter's comment.
As regards Grothendieck's opinion of Thomason's model structure, I do not know. Actually, I am unsure he knew of Thomason's model structure when writing Pursuing Stacks [EDIT: see Tim Porter's comment below]. What he knew for sure was that the localization of $Cat$ with respect to classical weak equivalences (functors between small categories the nerve of which are simplicial weak equivalences) is equivalent to the classical homotopy category. The first proof is due to Quillen and Illusie "wrote the details" (his words) in his thesis. (And there is a quite simpler proof, by the way.) Model structures crop up in Pursuing Stacks at some point, but I am pretty sure the idea is not developed in the beginning, which is much more concerned with mere models for homotopy types. Here is a citation from Chapter 75: "the notion of asphericity structure — which, together with the closely related notion of contractibility structure, tentatively dealt with before, and the various "test notions" (e.g. test categories and test functors) seems to me the main payoff so far of our effort to come to a grasp of a general formalism of "homotopy models"." (Beware: these asphericity structures are not what Maltsiniotis called "asphericity structures" in his own work.)
Another fact Grothendieck knew was, of course, Quillen's Theorem A. It seems he did not write a detailed proof of the relative version, but he gave a sketch of a toposic proof of it, though, and took it as an axiom for what he called basic localizer.
As for your second question, I do not know, but it seems to me that Grothendieck was not that interested in simplicial sets and thus did not work extensively with them. In a 1991 letter to Thomason, he wrote: " D’autre part, pour moi le "paradis originel" pour l’algèbre topologique n’est nullement la sempiternelle catégorie ∆∧ semi-simpliciale, si utile soit-elle, et encore moins celle des espaces topologiques (qui l’une et l’autre s’envoient dans la 2-catégorie des topos, qui en est comme une enveloppe commune), mais bien la catégorie Cat des petites catégories, vue avec un œil de géomètre par l’ensemble d’intuition, étonnamment riche, provenant des topos. En effet, les topos ayant comme catégories des faisceaux d’ensembles les C∧ , avec C dans Cat, sont de loin les plus simples des topos connus, et c’est pour l’avoir senti que j’insiste tant sur l’exemple de ces topos ("catégoriques") dans SGA 4 IV". (See here.)
To conclude, let me mention that, if one takes Grothendieck's viewpoint of homotopical algebra, there should exist not only a homotopy theory of categories, but a homotopy theory of $n$-categories. In this respect, there should be a "relative Theorem A" for every $n$, which should allow one to define a workable notion of "basic $n$-localizer". (Actually, this is already done for $n=2$: see this paper by Bullejos and Cegarra for Theorem A.) And then one should work out a theory of test $n$-categories, whose $(n-1)-Cat$-valued presheaves should be models for homotopy types, and so on. To sum up, what Grothendieck wanted to do amounts to giving new foundations for homotopical algebra, and this is still a work in progress.
David Roberts gives the two most useful available references in his answer. If you want to read Grothendieck's words (and in English), just wait for the upcoming annotated version of Pursuing Stacks.
EDIT (2013/10/29): Rereading this answer, I realize that I should add something of which I was not aware at the time of my writing, still regarding Grothendieck's knowledge of Thomason's model category structure (see also Tim Porter's comment and David Roberts's answer). An annotated version of section 69 of Pursuing Stacks is available at http://www.math.jussieu.fr/~maltsin/groth/ps/ps-69.pdf. On page 4, Grothendieck writes that "it appears very doubtful still that (Cat) is a “model category” in Quillen’s sense, in any reasonable way (with W of course as the set of “weak equivalences”". Thus, he was not aware of the existence of Thomason's structure then. See also note 6 on that same page: Grothendieck has learnt of the existence of Thomason's model structure between the writing of Sections 69 and 87.
Best Answer
I don't think I have a compelling answer to this question, but maybe some bits and pieces that will be helpful. One point is that all of the examples that you bring up are related to the first: simplicial sets can be used as a model for the homotopy theory of spaces. Pretty much any homotopy theory can be "described" in terms of the homotopy theory of spaces, just like any category can be "described" in terms of the category of sets (via the Yoneda embedding, for example). So if you've decided that "space" means simplicial set, then it's pretty natural to start thinking about presheaves of simplicial sets when you want to think about the homotopy theory of (pre)sheaves of spaces, as in motivic homotopy theory.
But that just brings us to the question "why use simplicial sets as a model for the homotopy theory of spaces"? It's certainly not the only model, and some alternatives have been listed in the other responses. Another alternative is more classical: the category of topological spaces can be used as a model for the homotopy theory of spaces. So, you might ask, why not develop the theory of the cotangent complex using topological commutative rings instead of simplicial commutative rings? There's no reason one couldn't do this; it's just less convenient than the alternative.
There are several things that make simplicial sets very convenient to work with.
1) The category of simplicial sets is very simple: it is described by presheaves on a category with not too many objects and not too many morphisms, so the data of a simplicial set is reasonably concrete and combinatorial. The category of topological spaces (say) is more complicated in comparison, due in part to pathologies in point-set topology which aren't really relevant to the study of homotopy theory.
2) The category of simplices is (op)-sifted. This is related to the concrete observation that the formation of geometric realizations of simplicial sets (or simplicial spaces) commutes with finite products. More generally it guarantees a nice connection between the homotopy theory of simplicial sets and the homotopy theory of bisimplicial sets, which is frequently very useful.
3) The Dold-Kan correspondence tells you that studying simplicial objects in an abelian category is equivalent to studying chain complexes in that abelian category (satisfying certain boundedness conditions). So if you're already convinced that chain complexes are a good way to do homological algebra, it's a short leap to deciding that simplicial objects are a good way to do homological algebra in nonabelian settings. This also tells you that when you "abelianize" a simplicial construction, you're going to get a chain complex (as in the story of the cotangent complex: Kahler differentials applied to a simplicial commutative ring yields a chain complex of abelian groups).
4) Simplicial objects arise very naturally in many situations. For example, if U is a comonad on a category C (arising, say, from a pair of adjoint functors), then applying iterates of U to an object of C gives a simplicial object of C. This sort of thing comes up often when you want to study resolutions. For example, let C be the category of abelian groups, and let U be the comonad U(G) = free group generated by the elements of G (associated to the adjunction {Groups} <-> {Sets} given by the forgetful functor,free functor). Then the simplicial object I just mentioned is the canonical resolution of any group by free groups. Since "resolutions" play an important role in homotopy theory, it's convenient to work with a model that plays nicely with the combinatorics of the category of simplices. (For example, if we apply the above procedure to a simplicial group, we would get a resolution which was a bisimplicial free group. We can then obtain a simplicial free group by passing to the diagonal (which is a reasonable thing to do by virtue of (2) )).
5) Simplicial sets are related to category theory: the nerve construction gives a fully faithful embedding from the category of small categories to the category of simplicial sets. Suppose you're interested in higher category theory, and you adopt the position that "space" = "higher-groupoid" = "higher category in which all morphisms are invertible". If you decide that you're going to model this notion of "space" via Kan complexes, then working with arbitrary simplicial sets gives you a setting where categories (via their nerves) and higher groupoids (as Kan complexes) both sit naturally. This observation is the starting point for the theory of quasi-categories.
All these arguments really say is that simplicial objects are nice/convenient things to work with. They don't really prove that there couldn't be something nicer/more convenient. For this I'd just offer a sociological argument. The definition of a simplicial set is pretty simple (see (1)), and if there was a simpler definition that worked as well, I suspect that we would be using it already.