Hmmm....I would say for a better Alpha Protocol....
1. Fix the graphical popups.
2. Let the player to design their own characters like in Mass Effect 2 (I know they were planning to do this but it was cut from the last minute...either they didn't have a female voice actor or the funds just got small for developing this game. They should of ask Jennifer Hale for that role.)
3. Better Gadgets, More spy weapons, and Spy armor.
4. Have a fully interactive world where its not like a hub or something and make it where u can explore the area without hanging around in the safe house all the time and give us more freedom.
5. Better Boss fights.
6. Have some fun picking out the music because in some stages the music don't play at all.
7. More ammo types, and realistic guns.
8. A better martial art system that allows the main character to learn different types from masters all around the world by complete side quests from each master.
9. Have a option to choose what type of dialog system you want. Like choose between from free moving (like not timed, like mass effect) and timed (the one that is currently being used in AP)
10. A better cover system.
11. A regenerating health system, I just hate the part where u hafta find those health stations and those midkits.
12. Having a totally huge branching story system that will allow to port your save files to the next alpha protocol game.
Thats my list for nao...I will add more stuff in when i remember some more stuff.