I think it's bad game design when a game promotes sameness. Being able to use the same proven build all the time is a flaw in a game like this, I think.
I agree - There's 2 games which I've seen recently which handle this well. The first is Dead State, the 2nd is Titan Quest. I'm not sure either method could be used in PP, but they give food for thought.
In Dead State your NPCs or 'Survivors' level up on a set path, however each NPC levels up in an individual way. There's a cast of 48 NPCs, some of which you'll find during a play through, others you might miss. (That in itself has the potential to make each play through different.) Each NPC levels up partially via a set route for that NPC, and particular through dialogue/interactions with the player.
*Spoiler for Dead State*
If Getz has a high enough Mood, he'll tell you his backstory: he was a teacher at a school with his fiancee, but a mistake lead to her death and those of many others. He will admit his grief and pain, and you can counsel him to deal with it (leading to the removal of his "Unhinged" trait), or suggest he focus even more on killing the undead (gaining him the "Undead Nightmare" trait).
The actual combat mechanics in Dead State is pretty much pap, but the characterisation is a strong point. You get invested in some of the NPC that you end up recruiting, others you just want to take into the wilderness and smash over the head with a shovel - I'm looking at you Todd Kantell.
Dead State is the first TBS game that I've played in a long time where I'm actually thinking about the individual NPCs as being anything beyond grunts, probably the last game where I got this feeling was Jagged Alliance. http://jaggedalliance.wikia.com/wiki/Marty_%22Kaboom%22_Moffat
In Titan Quest, it's a different genre; action RPG. But in terms of replayability you've got one of the most interesting level up mechanics that I've seen and I wonder whether PP could borrow some ideas from it.
When playing Titan Quest you have 10 different 'masteries' or classes that you can choose from in order to define the skills sets which will be available to your player, each of those masteries then has various perks which can be chosen to define your character's skill set. Applied to PP, just the fact of having 10 classes would be a vast improvement over XCom's 5, but where Titan Quest gets really clever is that it lets the player choose a first mastery at Level 2, and a 2nd one to combine with that first mastery at Level 8.
Oh wow, you now have a total of 55 individual classes!
1) Warfare + Hunting = Slayer
2) Warfare + Rogue = Assassin
3) Hunting + Rogue = Brigand
4) Warfare + Defense = Conquerer
5) Defense + Rogue = Corsair
6) Defense + Nature = Guardian
7) Hunting + Nature = Warden
8) Storm + Earth = Elementalist
9) Storm + Spirit = Oracle
10) Earth + Spirit = Conjurer
and so on, and so on....
Within each mastery you have a variety of perks that can be chosen when a player levels up, or you can choose to level up your bases attributes, and each perk can itself be levelled up multiple times. I've not played through to the end yet, but I'm heavily suspecting that the game doesn't give you enough level up points to level up everything, so you'll have to choose some perks to level heavily, and others to maybe just invest one or two points into.
There's a bit more explanation of Titan Quest's levelling system here.
Would it work applied to PP, I don't know - It might be so versatile that it leads to analysis paralysis, and it could be a nightmare to balance. But you'd certainly not get bored in trying out each of the combos, and your squad could have their class combinations pre-defined at the start of the game.
- This week I have been mostly playing Chaos Reborn.