The responsiveness of the UI in general has suffered greatly since the introduction of BAPI. Operations as simple as unchecking a mod can take 2-3 seconds to show a result, whereas prior to BAPI this happened instantly.
Daidalos has done some profiling here: http://forums.bethsoft.com/topic/1376871-rel-wrye-bash/pageviewfindpostp20839745
He's provided one small patch that was applied and appears to work, but obviously 0.5 sec out of 4.5 isn't going to fix it all. This needs to get looked into. The sooner it gets fixed the better. Large load orders are a major pain to work with.
r2402 from Daidalos to reduce lag by another 0.6 seconds.
This is frustrating, I think I've got this one fixed, but I can't attach files to a bug created by someone else. I'll have to post them to the forum instead.
Marking as pending since things appear to be going smoothly in Oblivion now. Plenty of patches have been applied to bring this under control.
MOVED TO GITHUB: https://github.com/wrye-bash/wrye-bash/issues/123