Final boss should have been... (spoilers)
I loved this game, completely different to the Metal Gear Solid games but still a lot of fun.
I was slightly let down by the final boss though, because I had read reviews before buying the game in which it was said that old enemies return and that the final boss's identity was a spoiler - which made me think it would be a character from the Solid games.
Especially since whe you defeat Sundowner he alludes to there being more at work than just Armstrong's plans.
I hoped that Armstrong would turn out to be Decoy Octopus in disguise. I know he died in Metal Gear Solid, but I'm sure they could have brought him back somehow - they brought back Solidus and Big Boss in part 4 when they were thought to be dead.
Even if not Decoy, then someone else who we have seen before. If they could have had it somehow be Solidus that would have been good, seeing as you fought him before as Raiden so to have a rematch would have been awesome.
Still, Armstrong was fun to fight.