Well, I'd actually say I'd like them to pay more attention to the writing. The developers seemed undecided as to whether Alex was supposed to be a sympathetic anti-hero (which I'd prefer) or a totally sociopathic killing machine. As soon as he seems to settle into one mould something happens that just makes you go "WTF". Yahtzee's bit about him running people over callously with a tank while musing "Gee, I hope I'm doing the right thing" was more or less right on the money with the writing in this game.
I thought the graphics were fine personally, people seem to not "get" that graphics have to be rendered in real time, and it's a batter of balancing graphics quality to the amount of things happening. "Prototype" is a very busy game, sort of like how "Saint's Row 2" is a much busier game than the graphically superior "Grand Theft Auto IV". The game has to track all those enemies, civilians, and heavily animated powers and be ready to draw them instantly if they come into sight. It's sort of like how in "Saint's Row 2"
, a typical moment could have you dealing with responses from a criminal gang, the police, and your own gang if you lead them into your territory. Substantially more going on, which means the graphics had to be lessened to allow for all of that. Hardware can only do so much. I would not want to see the graphics improved at the expense of reducing the amount of things that are going on, which is ultimatly what is liable to happen. Rather I'd like to see them spend the time tightening up the systems in place.
Also to be honest it would be nice if they stopped using the term "Parkour" because they thought it was cool. Every time I see him wallrunning and the game is referring to it as "super parkour" I want to yak.
More varied side quests would be good, and I also think they need to tweak the difficulty a bit. The game seemed to fluctuate heavily from too easy, to too hard. It did have a nice middle ground at times, but I felt that the situations where it seemed nicely balanced were outweight by times when it was weighted too far in one direction or another.