@Fire Fist:
Maybe I worded that wrong.
I'm not saying Ace is the final obstacle to overcome. But it wouldn't surprise me in the least that if, at the end of the arc, Luffy and Ace square off at least briefly.
If by square off you mean get into a little angry tussle like Luffy got into with Vivi during Alabasta. A full blown short fight like Zoro vs. Luffy or Franky vs. Luffy, between Ace&Luffy would be incredibly pointless. I could see him doing that with Croc before a bigger threat comes or the SN pissed luffy got them sent there, but not Ace.
@ZKaiser
I think it will be a small quarrel. Ace has shown that he wants to die to end the war (which is retarded),but the same result can be accomplished with his escape. Ace will most likely jump into Luffy's arms after a small bit of macho on Ace's part. The final Boss will most like be the Warden or Crocodile.
Forgetting about Garp, 5th level boss, 6th level boss, or even Momonga? Wouldn't be surprised if Akainu is waiting outside to escort Ace once they manage to get past all that too. Really can't see a poisonous diarrhea monster(who is the most likely 4th level boss) being the final baddie of this arc with so many known and potential big players present. Croc won't be the final boss for the same reason not to mention I can't see a previous final boss being one again just to test his skills vs. improved luffy. He may not even be one of the most dangerous pirate on Level 5, let alone 6.