It's now much easier to fight the MiB if you know how to. I made a radar base (just access lift + large radar system) on each continent, covering like 95% of the Earth's lands. Works well... at least for now.
What bothers me is that those little buggers tend to build their bases just outside of your radar coverage. Most of the bases I have destroyed so far were placed out of my radar range and some of them I found only by accident (following a UFO or going for other MiB base).
What's even more bothering, they can somehow build their bases on the water (or on one-pixel, non-visible islands), so if you won't spot and follow the initial UFO, which then spawns the base, then you're pretty much f***ed, since you got like 1% chance of finding the base later on somewhere in the middle of an ocean.
Base was somewhere between those two jets:
BTW, during this playthrough I haven't spotted those new aliens added by the mod (got plenty of them previously, though). It's more than half a year now and I didn't see even a single one... I just hope it's a bad luck, not some issue with the latest nightlies.