I'm right with you on energy savings, etc. Right now, the only PC in my home that's on 24/7 is a mac mini we use for a media server, and it's probably going to be replaced with something with less overhead soon. Plus, I don't want to lose data or lose the ability for the tank to send an alarm if/when the PC is down for updates, power outage, etc. I'm going to put my Arduino and network hardware on a UPS, so it can still tell me about an alarm condition if the home loses power. (That said, I've been living in this home for 8 years and have only lost power once, for a few minutes.)
Of course with modularity comes bloat and that's what I'm trying to decrease now.
Agreed on that, too. I haven't even thought about software yet, but on the hardware side, I tried to break everything into two categories:
1) Core stuff everyone would likely want - pH, an LCD, etc. I put this stuff on the main board.
2) Other stuff that's available or easy to do on shields.
I'm hoping to take the same approach with software. One core library that runs the onboard hardware, and people can tack on libraries if they want other stuff.
I guess the only "issue" that leaves is mixing and matching from different projects. If people like my hardware because it includes the LCD, but they like your keypad functionality, how likely is it that they'll be able to blend the two without issue? As the designers of this stuff, do we care?

It seems like there are a good strong 4 or 5 arduino based aquarium controller "projects" that people can follow right now, but they've all taken slightly different approaches.