This question appears to use some statistical terminology in unconventional ways. Understanding this will help resolve the issues:
A "signal" appears to be a (measurable) function $x$ defined on a determined Real interval $[t_-, t_+)$. (This makes $x$ a random variable.) That interval is endowed with a uniform probability density. Taking $t$ as a coordinate for the interval, the probability density function therefore is $\frac{1}{t_+-t_-} dt$.
A "sample" of a signal is a sequence of values of $x$ obtained along an arithmetic progression of times $\ldots, t_0 - 2h, t_0-h, t_0, t_0+h, t_0+2h, \ldots$ = $(t_1,t_2,\ldots,t_n)$ (restricted, of course, to the domain $[t_-, t_+)$). These values may be written $x(t_i) = x_i$.
The "expectation" operator $E$ may refer either to (a) the expectation of the random variable $x$, therefore equal to $\frac{1}{t_+-t_-}\int_{t_-}^{t_+}x(t)dt$ or (b) the mean of a sample, therefore equal to $\frac{1}{n}\sum_{i=1}^n x_i$. This lets us translate formulas for expectations of signals to formulas for expectations of their samples merely by replacing integrals by averages.
"Statistical independence" of signals $x$ and $y$ means they are independent as random variables.
The importance of powers of $\sin$ and $\cos$ becomes evident when we notice that "most" signals can be written as convergent Fourier series -- that is, linear combinations of the functions $\sin(n t)$, $n=1, 2, \ldots$, and $\cos(m t)$, $m=0, 1, 2, \ldots$, and that these functions, in turn, can be written as (finite) linear combinations of non-negative integral powers of products, $\sin^p(t)\cos^q(t)$. Because the expectation operator is linear, we would naturally be interested in studying and computing expectations of such monomials.
Now, $\sin$ and $\cos$ are usually not "statistically independent" except when the length of the interval, $t_+ - t_-$, is a multiple of $2\pi$. The signals of interest in applications are those for which this length is huge. Thus, at least to a very good approximation, we can think of $\sin$ and $\cos$ as being independent. But what does this mean? How can we think about it?
To discuss the concepts, I am going to make an "ink = probability" metaphor by considering scatterplots of large independent samples of $(x,y)$. If $A$ is any (measurable) region within the scatterplot, then the proportion of ink covering $A$ closely approximates the probability of $A$ under the joint distribution of $(x,y)$.
$x$ is plotted on the horizontal axis and $y$ on the vertical. $A$ is the rectangle. The proportion of blue ink drawn on this rectangle equals the proportion of the 2000 dots used, which reflect the joint probability density of $(x,y)$.
The statistical definition of independence of two random variables $x$ and $y$ is that their joint distribution is the product of the marginal distributions. The marginal distribution of $x$ is obtained by taking thin vertical slices of the scatterplot: the chance that $x$ lies between $x'$ and $x'+dx$ equals the proportion of ink used for all points in this region, regardless of the value of $y$: that's a vertical strip.
Now, in any vertical strip, some of the ink appears more in some places than in others. Compare these two strips:
In the right-hand strip in this illustration, the blue ink tends to be higher (have larger $y$ values) than in the left-hand strip. This is lack of independence. Independence means that no matter where the strip is located, you see the same vertical distribution of ink, as here:
What is interesting about this last figure is how it was drawn. It is a scatterplot of a sample $(x(t), y(t))$ at 10,000 equally spaced times. Let's look at the first one percent of this sample:
There is a clear lack of independence here! During any small interval of time, two signals can be highly functionally dependent, but if over a long period of time that functional dependence "averages out," the signals are still considered independent. (In this case the signals were $x(t) = \cos((e/20)t)$ and $y(t) = \sin(t/20)$ sampled at times $t=1, 2, \ldots, 10000$.)
Let's get back to the questions, which concern expectation as well as independence. We can also think of expectation geometrically: in a scatterplot of two signals (or their samples), $(x,y)$, $E[x]$ is the average horizontal location of the dots and $E[y]$ is the average vertical location. For instance, consider the signals $x(t)=\cos(t)$ and $y(t)=\sin(t)$ over the interval $[0, 2\pi)$, with this scatterplot:
The symmetrical form indicates the average of $x$ must be at $0$ and likewise for the average of $y$. Therefore $E[\cos(t)]$ = $E[\sin(t)]$ = $0$ (for this particular domain).
Consider now their squares. Here's the scatterplot:
Of course! $\cos^2(t) + \sin^2(t)=1$, so the squares must lie along the line $x+y=1$. The average of each coordinate is $1/2$. Naturally the averages cannot be zero: squares tend to be positive. So, if we wish to find the second central moment of (say) $x(t) = cos^2(t)$, often written $\mu'_2(x)$, then we first compute its expectation ($1/2$) and (by definition) integrate the second power of the residuals:
$$\mu'_2(x) = E[(x - E[x])^2] = \frac{1}{t_+ - t_-}\int_{t_-}^{t_+}\left(\cos^2(t) - 1/2\right)^2 dt.$$
In general, the $(p,q)$ central moment of a bivariate signal $(x,y)$, written $\mu'_{pq}(x,y)$, is obtained similarly: first compute the expectations of $x$ (written $\mu(x)$) and $y$ (written $\mu(y)$), and then find the expectation of the appropriate monomial in the residuals $x(t) - \mu(x)$ and $y(t) - \mu(y)$:
$$\mu'_{pq}(x,y) = \frac{1}{t_+-t_-}\int_{t_-}^{t_+}\left(x(t)-\mu(x))^p\right)\left(y(t)-\mu(y)\right)^q dt.$$
Continuing the example posed in the question, let $x(t) = \sin(t)$, $y(t) = \cos(t)$, and suppose the domain is a multiple of one common period of both signals; say, $[t_-, t_+)$ = $[0, 2\pi)$. As we have seen, $\mu(x)$ = $\mu(y)$ = 0. Therefore
$$\mu'_{23}(x,y) = \frac{1}{2\pi}\int_0^{2\pi}\left(\sin(t)-0\right)^2\left(\cos(t)-0\right)^3dt = 0.$$
More generally (in this case) $\mu'_{2m,2n}(x,y) = \frac{\pi ^{1/2} 2^{m+2 n-1}}{\Gamma \left(\frac{1}{2}-n\right) \Gamma \left(-m-n+\frac{1}{2}\right) \Gamma (2 m+2 n+1)}$ for non-negative integral $m,n$; all other central moments are zero. (This formula in terms of Gamma functions works for non-integral $m$ and $n$.)
A subtle and potentially confusing point concerns what we consider $x$ to be. If, instead of taking $x(t)=\sin(t)$, we consider the different signal $x(t)=\sin^2(t)$, then, as we have seen, $\mu(x)=1/2$ and therefore
$$\mu'_2(x) = \mu'_2(\sin^2(t)) = \frac{1}{2\pi}\int_0^{2\pi}\left(\sin^2(t)-1/2\right)^2 dt = 1/8.$$
Beware: because the expectation of $\sin^2$ is nonzero, its second central moment, $1/8$, does not necessarily equal the fourth central moment of $\sin$ (which equals $3/8$), even though both integrals involve fourth powers of $\sin$.
Finally, when working with samples, just replace the integrals by averages.
Since the question was updated, I update my answer:
The first part (To compute the skewness, why not standardize both the mean and the variance?) is easy: That is precisely how it's done! See the definitions of skewness and kurtosis in wiki.
The second part is both easy and hard. On one hand we could say that it is impossible to normalize random variable to satisfy three moment conditions, as linear transformation $X \to aX + b$ allows only for two. But on the other hand, why should we limit ourselves to linear transformations? Sure, shift and scale are by far the most prominent (maybe because they are sufficient most of the time, say for limit theorems), but what about higher order polynomials or taking logs, or convolving with itself? In fact, isn't it what Box-Cox transform is all about -- removing skew?
But in the case of more complicated transformations, I think, the context and the transformation itself becomes important, so maybe that is why there are no more "moments with names". That does not mean that r.v.s are not transformed and that the moments are not calculated, on the contrary. You just chose your transformation, calculate what you need and move on.
The old answer about why centralized moments represent shape better than raw:
The keyword is shape. As whuber suggested, by shape we want consider the properties of the distribution that are invariant to translation and scaling. That is, when you consider variable $X + c$ instead of $X$, you get the same distribution function (just shifted to the right or left), so we would like to say that its shape stayed the same.
The raw moments do change when you translate the variable, so they reflect not only the shape, but also a location. In fact, you can take any random variable, and shift it $X \to X + c$ appropriately to get any value for its, say, raw third moment.
The same observation holds for all odd moments and to lesser extent for even moments (they are bounded from below and lower bound does depend on shape).
The centralized moment, on the other hand, does not change when you translate the variable, so that's why they are more descriptive of the shape. For example, if your even centralized moment is large, you known that random variable has some mass not too close to mean. Or if your odd moment is zero, you known that your random variable has some symmetry around mean.
The same argument extends to scale, which is transformation $X\to cX$. The usual normalization in this case is division by standard deviation, and the corresponding moments are called normalized moments, at least by wikipedia.
Best Answer
You are in essence looking for a multivariate measure of skew and kurtosis. There are many. I would start with the most establish ones, which are the multivariate skew and kurtosis measures of Mardia 1977 [0].
It seems to me you are more asking for an implementation than about the measures themselves. I don t know of any matlab implementation, but the R code below (from the R library psych) should be fairly easy to translate in matlab: