I would say that as long as you keep the system simple, everything is going to be fine. Here’s my idea:
First of all, to Blitz, Live and Correspondence time controls I would add at least two more in the Open Challenge box. For example, Blitz, Fast, Normal, Slow and Correspondence. Each of them having a default time setting in preferences.
So, when creating a challenge, there would be some modifications.
- All the fields fields except the specific time control parameters are unblockable. If you block all of them, you have a conventional open challenge. In particular, if you block game speed and time control, then you can specify the exact time parameters.
- If you unblock some of them, the system will try to pair you with the following condition: All your blocked fields must be equal or unblocked in you opponent.
- When the server finds a posible match, the negociation phase let the players change only the fields that both players had unblocked. This is done like @crodgers said. Being: first the challenger sets his preferences and sends them to his opponent; then he accepts or modifies them and send them back again to the challenger; and in this last case the challenger accepts or rejects them. If he rejects, they’re back again in the queue.
- Correspondence games can’t be automatched. In my opinion, it’s not necesary to make an automatch system for correspondence games. Besides, OGS already has a large flow of correspondence games and the system works just fine, and I’ve never heared someone wanting it for that matter.
- The option pause on weekends is only available for correspondence games, so it’s not unblockable.
- Ranked games should have handicap, color and komi fixed at automatic and analysis disabled.
Maybe this system is simple to me but not for most people, so please be critical in your feedbacks. 
EDIT: I added point 6.