For my personal use, I never go over 128x128, but something like 512x512 would be huge if you are planning to use the HD mode, as it would take 2048x2048(!) frames. We will most likely add it as an option but with a huge, red, capital warning.
I understand where you are coming from. It might be wiser to keep the use of a tool like this for small sprites, and for anything super large use tweens etc. Maybe a middle ground 256x256 would do.