Final Boss *spoilers-ish*

[wallacethepig]

The penultimate fight will be a test of your team.  The final fight will be a test of your solo build.

I would reverse this. You fight something off, only to have your friends come help you out for the final battle. You make the player think they'll have to fight the final boss alone (because they fought the penultimate boss alone), but then your friends show up to help you out. That could be a bit of inspiration for teamwork.

Alternatively, you could kill off all the party members one by one until the MC finally takes it upon himself to face the big bad guy all alone.

The real problem with having a team for the whole game and then getting rid of it is that it throws all that grinding you did to make your mage/beserker better. It's kind of like giving a player a bunch of items to help them throughout the game and then taking them all away when you fight the final boss. So all those Full Potions and Elixirs are now useless. It just makes people mad, is all I'm sayin'. However, if the player chooses to go solo, he will feel a great sense of reward when he finds out he may have made the choice that wastes less time.

-Wallace

 

[Eschaton]

I guess it all depends on the story, in the end.  For example, all of you expect some armored mastermind in a tower or Lovecraftian dimension somewhere.  That's not the case.  Not at all.

 

[Omnimental]

KOTOR was awesome, it really was.  But if you were a "talk or sneak your way out of every battle" Revan, than Malak would own you.  The infinite droids in the Star Forge would own you.  And the game encouraged non-combat builds.  If the game suddenly changes their mind in the final level, that's bad design.

As someone who totally enjoys playing the avoid-combat style character, it was more than a bit frustrating.  Amazing game, just a small part of godammit-how-the-!@# near the end.

 

[ArchaicSpoon]

Storytelling-wise, it can work provided that the back-story/reason for the duel is good. I mean, the protagonist shouldn't just go "Hey guys, can I please try to solo this galaxy-devouring demon? I want the final battle in this game to be an epic one!" and needs to have a good reason, such as having the rest of the party incapacitated(though, this seems a little forced) or having personal matters between the hero and the villain, causing them to prefer to duel rather than a fight against the whole party.

Game-play wise I see two problems. The first one would be that in case your game allows a ton of customization, what if the player turned the hero into a completely supporting class? It'll be kind of impossible to complete the game when you need to solo the final boss with a priest/white mage. The second problem may happen when you allow the hero to be swapped out without any spill-over experience. If the player ends up switching the hero out in the beginning, he'll pretty much have to face the final boss with a level 12 undergeared character, which is kind of frustrating. So as others have said, I'd say that I'd do this in a 2-part battle where first it will be the party versus the villain, and then an easier one with the protagonist versus the villain.