Fusion categories (over $\mathbb{C}$) are a natural generalization of finite groups and their behavior over $\mathbb{C}$. The complex representation theory of a finite group is a fusion category, but there are many others. In fact, you can think of a fusion category as a non-commutative, non-cocommutative generalization of a finite group. A finite-dimensional Hopf algebra is that too, but they don't have to be semisimple, while the semisimple ones give you many fusion categories, but again not by any means all of them.
Many of the basic results about the structure and representation theory of finite groups generalize, or seem like they could generalize, to fusion categories. This principle has been worked out to a very incomplete but interesting extent by Etingof and others. For instance there is an analogue of the theorem that the dimension of complex irrep of a finite group $G$ divides $|G|$. (Addendum: A qualified analogue, as Scott and Noah point out. If the category is braided, it is a strict analogue; otherwise it is an analogue of dividing $|G|^2$.) There are also semisimple Hopf algebras and other fusion categories that look a lot like $p$-groups.
You can think of the whole theory as a rebooted theory of finite groups. However, we are miles and miles away from any fusion category equivalent of the classification of finite simple groups. It is a struggle to make fusion categories that are not derived very closely from finite groups, or do not come from quantum groups at roots of unity. Only a few types of examples are known, and who knows what else is out there.
One enticing thing that does change is that dimensions of irreducible objects in a fusion category don't have to be integers. For instance, one of the simplest fusion categories is the Fibonacci category. It has two irreducible objects, the trivial one $I$ and the other object $F$. The dimension of $F$ is the golden ratio, as you can infer from the branching equation $F \otimes F \cong F \oplus I$. (But the dimensions are algebraic integers, and even cyclotomic algebraic integers. Hence divisibility is still a sensible question.)
You could also ask, why the semisimple case. As you learn in undergraduate or basic graduate representation theory, the semisimple representation theory of a finite group is much cleaner than the modular representation theory in positive characteristic.
And yes, you also get 3-manifold invariants and subfactors.
For references: Really Turaev and Viro's original paper, state sum invariants of 3-manifolds and 6j symbols, is pretty good. The generalization to spherical categories is due to Barrett and Westbury, Invariants of Piecewise-Linear 3-manifolds. And there is a discussion in Turaev's book.
A sketch: Recall that a basis-independent expression in tensor calculus has the structure of a graph with vertices labelled by tensors and edges labelled by vector spaces. A monoidal category allows the evaluation of similar expressions, except that the graph must be planar and acyclic. In a rigid pivotal category, there are good duals and the graph just needs to be planar. In a spherical category, left trace equals right trace, so a closed graph can be drawn on a sphere. If it is spherical, rigid, and semisimple, then you can use the graph of a tetrahedron to make a local interaction on the tetrahedra of a triangulated 3-manifold, and the result up to normalization is the Turaev-Viro 3-manifold invariant. (In this setting you should dualize the tetrahedra, so that a tensor morphism in the category is associated to a face of the tetrahedron.)
The cyclic subfactors theory defines a too large class$^{\star}$ of subfactors for being an good quantum arithmetic (i.e. quantum generalization of the natural numbers theory).
Nowadays, my better attempt for this is the natural subfactors theory (see the optional part here).
$^{\star}$Up to equivalence, more than $70$% of the inclusions of groups of index $≤30$ are distributive lattice! Nevertheless the percentage is decreasing for the following indices (see this post).
Question 1: No, $(R^{A_7} \subset R^{S_4})$ is a counterexample.
Thanks to the subgroups lattice of $A_7$ (see here), there is a subgroup of $A_7$ called $2^2:S_3$ isomorphic to $S_4$, such that $(S_4 \subset A_7)$ has exactly two non-trivial intermediate subgroups: $K=L_2(7)$ and $L=A_4:S_3$, so that $(R^{A_7} \subset R^{S_4})$ is cyclic.
Now if we consider the two maximal chains $(S_4 \subset K \subset A_7)$ and $(S_4 \subset L \subset A_7)$, then the intermediate indices are $(7,15)$ and $(3,35)$, so these chains can't be equivalent.
See the questions: Jordan-Hölder theorem for subfactors? and Abelian subfactors, a relevant concept?
Question 3: No, the maximal subfactor $(R^{\mathbb{Z}_3 \rtimes \mathbb{Z}_2} \subset R^{\mathbb{Z}_2})$ gives counter-examples.
It is depth $4$ and it admits several compositions with itself which are also cyclic subfactors of depth $4$,
for example $(R^{(\mathbb{Z}_3 \rtimes \mathbb{Z}_2) \times (\mathbb{Z}_3 \rtimes \mathbb{Z}_2)} \subset R^{\mathbb{Z}_2 \times \mathbb{Z}_2})$ and $(R^{\mathbb{Z}_9 \rtimes \mathbb{Z}_2} \subset R^{\mathbb{Z}_2})$.
Their intermediate subfactors lattices are as $\mathcal{L}_6$ and $\mathcal{L}_4$, so they are not isomorphic.
($\mathcal{L}_n$ is the lattice of divisors of $n$).
Best Answer
If you want to understand some collection of objects, naturally you should also want to understand all maps between them. Since factors have no two-sided ideals, every map between factors is an inclusion. So to understand maps between factors is the same thing as understand subfactors. (This is a way in which factors are noncommutative analogues of fields, and hence subfactors are a noncommutative version of Galois theory.)
Also since all vN algebras are direct integrals of factors, understanding subfactors is the only interesting part of understanding all maps between all vN algebras.