The first game was rife with issues, but none that couldn't be fixed and all-in-all the game was good fun.
Major issues were the story and the amount of gunplay: not enough (not enough that was good anyway) and far too much, respectively. The first step to fixing the story would be scrapping those fucking awful animated cutscenes; the game's beautiful, just play normal cutscenes using the engine.
Minor issues were things like making me twist valves for no reason. There I am, sprinting from the police, when some steam gets in my way so I have to break all momentum (and excitement and adrenaline) to turn a valve.
Likewise in terms of the combat, I want to be sprinting across the rooftops at full belt, leaping down 2 stories (Assassin's Creed 2 completely nails that) at some points. I don't really want first person platforming in the sense that I hold onto a ledge and shimmy across.
It definitely needs a sequel; the idea's too good to just leave behind as a "failed" experiment.
Oh, and add a multiplayer where we can race each other for fuck's sake. Honestly, how could you leave that out but then include a rather dull time trial mode?