I have to say, I'm with TheBrainGuy
I really, really enjoy this game, but I too have some thoughts;
Online Multiplayer - Play against others solo or with a team
A bigger storyline (xD, as also quoted)
A few optional bosses like Mag Agent: Torture
alongside, more basic enemies like Mag Agents (v2 specifically, came to my mind)
Ability to play as a few different characters (Don't get me wrong, I absolutely love the Character-build idea, but it's just a thought)
I could go on and on, but I'd rather play the game more now.
Keep up the good work!