the reason I like the progression system in torchlight 2 is the flexibility. there aren't a thousand skills to choose from, but the tier bonuses mean that you can tailor your play style around your choices, as well as having skills which are largely situational abilities that still remain useful throughout the game because they scale with level.
then there's the huge number of different stats on gear, and gems of course. something which seems quite minor can make a big difference over the course of the entire campaign, because you begin to evolve your play style around it. add in enchanting and the fact that you can swap gems in and out, and you can design a wide range of gear sets for different circumstances.
the way the attribute points are designed is pretty ingenious too. someone was wondering about why strength and not dexterity affects ranged weapon damage earlier in the thread, I think it's just so that there isn't a single completely useless attribute for any character. they all use mana, have hp, gain white damage from strength and crit more with dex.
and of course there's spell scrolls. I found one a little while ago which increases my resistance to movement impairing effects by 25% passively. again, that's a really clever and flexible way to give players more ways to customise their build so it's truly their own.
even pets are hugely influential to your build and play style, both their load-out and how you choose to use them. if you load your pet up with heavy armour and offensive spells, then leave it on aggressive, you have a fairly competent pocket tank. load it up with buffs and heals, then put it on passive, and you have a little support unit following you around and looking adorable.
so yeah, I like it quite a lot.