Just to clarify, we've actually started on the macro language / API thing for Foldit. There's a grad student working on it. It's going to happen.
I think it is reasonable to want all the hotkeys as easily accessible as possible. The best solution I think would be to have user-definable hotkeys, which should resolve all past and future hotkey-related complaints. In the meantime I may change the New Best default hotkey, or add a second hotkey to it.
How about a switch in general options, similar to the one that switches right click/middle click?
The switch will change a/ctrl-b with ctrl-n.
One mode will allow users to keep things the way they are, ctrl-b is always "very best" and ctrl-n (or some better hotkey) is the current best.
While the other mode (like the dev preview) allows you to set ctrl-b as "current best" and use another hotkey or the undo buttons if you need to restore your "very best". the second mode would probably be more usefull if you feel stuck and must restart, ctrl-b and A would then function as the "current best" for that new start.
Customizable hotkeys would solve all of these problems in the long run,but a switch should be something that can be thrown in the next update with little work.
that's a reasonable solution for the interim, until the developers include player definable hotkeys.
All shortcuts in help :) Closing.