Admittedly, I haven't actually played Agent of Providence myself due to circumstances beyond my control (budget mostly) that said I have watched a full walkthrough, and it is a excellent first installment of a video game franchise, it's fun to play that's the main thing. However for a sequel they can do better and here's how I think that can happen.
- More levels greater play time, I'm thinking Mexican village (specifically the one featured in Night Falls) Aquania, The Bug Jar, Paradise Base, Petting Zoo, Abysus, Hong Kong, Greenville Ohio, Gabriel Rylander's lab, and the desert featured in Written in Sand.
- Puzzles, lots of puzzles, specifically puzzles unique to Rex's machines (Ex: Smack Hands used to turn gears, BFS to hack obstacles, Slam Cannon to nail far off switches, manipulate the enviroment with technopathy).
- A Cure mechanic, collect DNA from E.V.O.s, bring that DNA to Cesar and Holiday, they develope a cure for that E.V.O. species and they put it into Rex, and Rex turns that into a finisher move against that specific E.V.O. species (with added bonus of a little E.V.O. gallery in Holiday's lab) giving him a greater Nanite boost.
- Side missions, with consequences shown in post credit scenes (Rex goes after Biowulf in the Village instead of Hunter Cain and he is able to build a purifier styled army as a consequence).
- Unlockable Memories, Rex finds a item from his past and as a result unlocks a reviewable memory from his past (Rex finds a news clipping of his full E.V.O. form and he unlocks a memory from the time that Six saved him when they first met).
- Assist characters, complete a level, get a assist character super move (Agent Six comes in and uses magna-blades to magnetically toss E.V.O.s into the air and smash them into the ground).
- With all these features rolled into one budget must give somewhere, namely variants on basic enemies, such as normal, Juiced, and Amped.
Any more ideals for gameplay is welcomed, ideals for plot wanted, and maybe, just maybe, if someone at D3 is listening, they might end up in game.