So it seems that one of the big reasons for simpeed issues is the massive assist by T1 engineers on factories. BRINK said he confirmed this by ctrl-k'ing all T1 engineers and simspeed jumped from -2 to 0 or something in that order.
Then I saw this video by ZLO in which he shows what happens when you assist ground with engineers. They stop colliding and playing bumpercars. They also align perfectly:
http://youtu.be/Hpf1OaCEsyc?t=47m7s
Now perhaps there isn't a direct connection between engineers bumping into each other / pathfinding and simspeed. But just making them never collide seems like a good idea anyway. Bumping engineers are probably the biggest annoyance in the game, considerably slowing your expansion. And just image if it would increase the simspeed by one or two points as well.