I'll have to try it out next time I need to get anywhere (which will be soon) but just clicking through you appear to have the two things I really need: a one-click spot for nearby stops of all transit (well, you've got Muni and BART but that's both a good start and the majority of my transit) and the ability to save frequent stops. The ability to check buses around a given stop is also something I've been wanting, though less often.
I don't know if you're planning any of this already but I do have a couple suggestions based on my current frustrations with nextmuni:
1. Favourite buses in addition to favourite stops and prioritise said buses when nearby. I know that 21 and 5 are the two best buses to get me home but when I'm downtown they often aren't even on the nextmuni's nearby list because of the density of buses. I'd love to be able to favourite those buses and have them show up first (or at the very least always show up) if a stop is sufficiently nearby even if I'm at a stop I don't frequent.
2. This one would be a bit more of an involved feature and I'm not sure how feasible it is with whatever dataset and/or APIs you have to work with. Basically, I want to be able to input my destination and have the site serve me buses with stops near both end points (if any exist), giving me time estimates near my current location.
Configuring "nearby" would be handy but far from critical, also.