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I believe that Saito would win. Mainly because Saito would not ingage in a fair fight. He would assassinate Aoshi when the best opportunity presented itself.
However he would also be likely to win in a duel because of a few reasons. First, he would probably make Aoshi angry and emotionally unstable by making him relive the deaths of Bashimi, Hyottko, Hanya, and Shikijo. He would also rub Aoshi's wound concerning his failure to become the strongest. Secondly, Aoshi has not seen Saito's final attack and even with his defensive expertise he would not be able to block it, seeing as that it is likely that even Kenshin would not be able to dodge it. This reason is mostly based off of the fact that Saito would not have wanted to save that attack for Kenshin if he did not believe that he could kill him with it. Thirdly, Saito is a master of using his environment and cornering his unsuspecting opponent. An example of this is in his battle with Kenshin where he uses his own belt and jacket almost as well as his katana. Most people forget that Saito is a genius of battle and has likely fought more then Aoshi and against opponents that are equal or more difficult then the opponents that Aoshi has battled. At worst the fight would be even an both would likely die, but Saito is more likely to win.

I think the fight between them both would be very balanced. Saitous Gatotsu is very effective and on the other side Aoshis attacks like Kaiten Kenbu are very powerful too.

The Oniwabanshu beating the Jupongatana O_o?!? Who voted on THAT one? Sojiro could destroy the entire Oniwabanshu by HIMSELF (not including Aoshi), and could probobly kill aoshi in a one on one fight. WOW. Did these people even watch the anime, or do they just think Aoshi's hot?

That's a very tough choice... I can't seem to decide right now either! neutral

^ eek this is sort of a speak of the devil kinda thing, neh? wink ^

My choice in this is pretty obivious, neh?
Might as well be clear anyway, Saito would win.
He was about a million different things that give him the natural advantage, even being left handed is a positive for him.
He of course is an excellent manipulator, and not limited to conventional fighting.
Then of course remember those nasty lil steel doors our heroes were stumped by... the ones Saito Gatotsu'ed his way through just after being K.O.'d and while having some terribly difficult injuries.
BTW don't underestimate the severity of those wound on his legs, the fact that he managed to hit Shishio with wounds like that... impressive.
Let's also not forget that had Shishio not been wearing a concealed forehead guard... it would have been a one hit kill scored for Saito.

Aside from all that Saito was also the first to recover. While Kenshin healing, and Aoshi was attempting to work out his issues. Saito was getting set to head off on another mission.

I would have to choose Saito he's much wiser an quicker than Aoshi i think