I'll admit that my priorities are probably different from the majority of gamers, but this is my wishlist.
1. An option to display full text of dialogue choices, rather than the current summary wheel. I don't know why it was decided to go with Mass Effect-style crapshoot dialogue choices rather than a more traditional format, but it is by far the biggest thing impacting my enjoyment of the game. (I suspect there is near-nil chance that this will happen.)
2. Related, but bring up the dialogue choices (and the timer) when the NPC finishes talking, rather than when they start. Why am I asked to reply before I know what I'm replying to?
2. As others have said, character customization should be prior to game start. That seems like a no-brainer to me.
3. Hacking minigame needs serious work on PC. As-is, it's nearly unworkable. (I wish this game had some sort of tracking like Steam did for HL2, just so we could see how many PC players gave up when they reached the hacking bit at the end of the tutorial level.)
4. As others have said, allow saves anywhere, rather than using a checkpoint system. It's 2010.
5. Optimization, bug fixes, AI, etc. Honestly, for me these are far less pressing than the above issues. I will cheerfully tolerate an RPG that has bad combat mechanics, poor performance, and bugs - provided I find the dialogue and story aspects enjoyable. In Alpha Protocol, as it is now, I do not enjoy the dialogue and story aspects because of some very poor choices in how they were handled.
