This is a topic that I've seen discussed often (especially back in Season 1.) Quite often, the verdict was that Peter would most certainly win, despite Sylar's heightened ability to see how the ability works, because of his advantage in how he gets abilities. But as I was reading through the web comics and watching old episodes, something interesting occured to me...
PETER
Peter can use only one ablity at a time, as he was taught by Claude. Otherwise, he begins to lose control and, well, we get wigged out Peter (OVERLOADDDD!!!) Mind you, this only applies to abilities which rely on focusing and motivation to be well utilized. Automatic abilities, on the other hand, happen... automatically? Hence, Peter can currently use any one of his powers, and at the same time regenerate.
Example of powers that can be dubbed "automatic"so far on the show: Regeneration, Super Hearing, Super Memory, and Super Strength. While the latter three can be controled to an extent, the first is truly unstoppable (unless one consciously shoved something sharp in the back of their neck before a fight... or blew their head off... but then they'd just be dead :D)
Other abilities falls into the "consiously controlled" category. While they may have manifested without deliberation initially, these powers require focus to use well. (Think of the "Hiro" face.) Afterall, we wouldn't want Hiro thoughtlessly warping time, would we?? O.O
Also, there are abilities which fall somewhere in the middle. These are possibly dangerous to Peter. The only ability which truly falls in this category seems to be the nuclear power. This power could be controlled consciously to a large extent enough for it not to truly be automatic, and even turned off, but can be triggered or grow in intensity without the users consent. This is what makes it so dangerous to anyone, and ESPECIALLY dangerous to Peter. (Also, the fact that Peter had super strength and the nuclear power activated at once is what validates the super strength as automatic. At that moment, Peter had use of two automatic powers and one conscious one. Naturally, with that one conscious power activated, the only things he could have done without losing control and decimating New York was... continue naturall regenerating or start punching things. Good luck with that one, buddy.)
However, Sylar doesn't have to deal with this, because...
SYLAR
Sylar has two large advantages: he can control his abilities to a far greater advantage than Peter because of his naturalability to see how things work, and can use all of his powers at once. Perhaps this last part is because he is able to "see how it works" (referring to the powers, his brain, and his body) to use more than one conscious ability. (Sylar's power also had enough oomph in it to keep the semi-automatic ability that was the nuclear power at bay, though he struggled to completely focus his super hearing right away; however, he certainly pulled it off quickly.) However, I think that the reason that Sylar can use all of these abilities at once is because his method is more full proof than Peter's; while Sylar is manually changing the makeup of his brain and body with a perfect level of intuition behind him, Peter is just copying abilities, because that's what he does. He is able to use one focused ability at a time, which is probably the evolutionary limit. Sylar, on the other hand, is truly pushing the limits of evolution, achieving the ability to use an assumably infinite number of stolen powers at once. Peter, on the other hand, is just an empath, and it is strongly implied by Claude that these are nothing new. Sort of brings new meaning to all those creepy things about "evolutionary imparitive" that Sylar says, eh?
So, I belive that Sylar and Peter are evenly matched in terms of advantages and disadvantages:
Peter can use any conscious ability he has absorbed, but only one at a time, along with any "automatic" ability he has. He can also obtain these abilities with the simplest of ease.
Sylar, on the other hand, can use ANY ability he has stolen, pulling as many out at once as he wants, and can control them all at an enhanced level due to his understanding (this applies to his "snow globe" stunt he showed to his Mother.) But he has to hunt and kill to get 'em.

