After a couple of days thinking on it, I'm pretty sure the Mac App Store (MAS) will be a good thing for Flying Meat in the long run. It's my intent to have both Acorn and VoodooPad up there as soon as possible, assuming Apple will approve my apps.
There are of course some things that really bug me about the MAS, the big one being the 30% cut that Apple takes from sales (lots o' money to Apple, and I'm paying to be a Mac Dev? How about a cap?) and of course the problem of not being able to charge for upgrades is a pretty big deal to indie devs.
Will Apple resolve all the problems folks like myself have with it? Unlikely. Will FM be obsolete in a few years if I don't get on the Mac App Store? Probably.
I do worry that someday the Mac App Store will be the only way to get apps, and I worry about my friends who have applications which I know will never be approved on the store. Time will tell how things shake out, and I'm hoping for the best.
P.S. At least we have real game controllers on the Mac.