I don't know if we're in a place to change the rules for timing at this point, but if so, I like the idea of using only IGT.

Using IGT would reward creative use of time-manipulation abilities (like in R60D's 01Aug run that is in 3rd place under the current leaderboard setup) and therefore would be a nice way to celebrate a mechanic that sets this game apart from other shoot-'em-ups.

I don't have the tools to test if lag affects IGT, but it almost definitely affects RTA.

The one disadvantage I see, aside from the work of re-verifying past runs, is that IGT does not tell fractions of a second and would complicate comparison of close runs.

All that said, time for me to actually learn how to use timebreak :)