As much as I love this game with all my heart, I have to admit this game has some pretty severe flaws, and on the road to the steam release, I'd like to propose a checklist of things that need fixing, from most severe to least severe. For the record, I was The Hobo King on the Greenlight page.

More detailed graphics options. I'd kill to be able to turn off things like AA or the filter effects, or fiddle with the FOV.
Mouse driven menus.
Client or launcher graphics options.
Gamepad binding/alt control schemes. The default ones can get a little awkward.
Further clarification of what agents can use what weapons. That one really screwed me over at times.
Less awkward holdups.
Keeping a crouched agent crouched when given a move order.
Make the spy silent, as it's really weird having guards following the spy for no reason, and makes it awkward to pull off some rescues.
Reworking the rat objective. It feels a bit RNG as well as being annoying on a pacifist/stealth run.

Nice to haves/somewhat difficult requests.
Less suicidal pathing.
Making the puzzles optional. I felt that they were good, but they screwed with the pace of the game.
Rework the spy's pull, it's crazy exploitable. A brief "Look, a distraction!" or something like that might be cool.

I understand the massive amounts of bad luck and hard work that have gone in to this game, so I can sympathise if you guys can't deliver on some of these. All the best.

I share your feelings regarding the flaws, but the biggest one that bothered me was the size of the monitors. More agents = less size of the monitors and I usually don't like a small monitor. This game would have been perfect with a multi-monitor setup so you use one agent per monitor or perhaps 2 agents per monitor. With one monitor I would have preferred to have one large (or at least customized) and the less small, using the non-active agents as 'look outs' or basically spy cameras.

I agree about the graphics, definitely a choice for the filters, AA, view distance, FOV etc.. Hopefully they could revitalize some at least in case the Steam release is a success.

And yes, rework or decrease the effeciency of the spy's distraction ability. Also add a silent effect, both for aestetics and as gameplay element.

Thanks both of you for the detailed feedback. We will try to get as many improvements into the next update as time allows.