I have no idea what else Evan is currently working on, but I'd rather get on with IX and other stuff than spend weeks overanylising this issue. Denominate down to 0.1 or 0.01, bloat be damned, we have time to deal with it if it ever gets to be a problem. What merchants are going to be selling anything in units of less than 0.01 anyway?
Stick a warning popup in the client if a user tries to spend linkable change. Maybe make the auto input choosing a little bit smarter. Move on.
edit: Also, what moli said - make the coin control thing more obvious, make it a routine part of the process. You open your guvpaper wallet, you choose which notes and coins to take out, same thing.