I feel like the challenge tasks added in update 1.07 could improve the run time. You pretty much get free staff and GMP for doing mundane tasks.

what are the challenge tasks?... and why would they improve the time? staff and gmp are not needed for any% first mission... or for ng+

how would it save time? on which category?

I'd have to look at the list more closely, but my guess is it wouldn't affect anything. In any%, there's no reason to go out of your way to get anymore gear, since you can get everything you need naturally just by finishing the missions.

The new Level 9 upgrades, from what I've seen, don't look that much better or useful than any other equipment, so I don't think IL or NG+ runs would be affected either. But I'd have to take a closer look.