The thing is...
Yes, more of what everybody else said, reloading was annoying, the graphics need work, "Mr. Bad" isn't creative, and not in a stylish way either.
But, even if you had a great storyline, amazing graphics, and a different reload system, AND levels, this is still a boring type of game that has been done a thousand times over, so I'd just drop this whole series if I were you and move onto something a bit more innovative next time.