"both being stealth shooters from a 3rd person perspective, both being released in fall 09", and i'd class the difference in end results from independent game developers and huge game factories as being a judgement call, PoP and AC were two of the most popular and well received games in recent years, and while i didn't enjoy either of them i respect what they did in terms of gameplay and story, i'd go so far as to say that both were experimental, something you wouldn't have seen from one of the giant publishers/developers 5 years ago
Just so you don't get me wrong. PoP and AC are incredible achievements, especially in the art department. But ultimately when it comes to gameplay and story, Obsidian will clearly win.