Most likely because FC never intended for a new server to be put online, and when AI was designed, didn't account for that at all - that is, they didn't build in a manual way to set and configure research. Therefore, the easy way out was to go, "Hey guys, time to do some global research! "
But the player blacklash has made them reconsider and begin to re-evaluate things on their end, as you can see in Vhab's post above me, research is currently broken on test. This implies to me that they are trying to come up with a way to set it to certain levels or thresholds.
Why did this not happen when RK3 was merged onto RK1 and RK2? Simply because that was nothing more than duplicating characters onto a new server and shutting down the old one. With this upcoming merge, RK1 isn't being moved onto RK2 and RK2 isn't being moved onto RK1. They are being combined and being put on a completely new, freshly installed, server.