Rooting stock doesn't cause an update issue unless you start deleting bloat and stuff. Freezing it is better, but that can be done via JB anyway. My personal favorite thing to do with root was to adjust the LCD Density, so everything was much smaller on the screen. Stock looked way too large imo. Of course this causes an issue with the play store, so yeah, more issues abound.
But yeah it works, don't think I've seen anyone have an issue. The sad part is, Rosenberg says that he might quit working on Moto devices since the exploits are becoming too difficult to find. So I guess if you don't do it before the update, you might be SOL in the future. Can't really blame the guy though. Fortunately rootkeeper kept root through the OTAs so far, so hopefully that keeps working.
CM10 was using both cores but I don't know really what the hell it was doing. I think it was keeping them both on at all times, since my battery life was atrocious. It's just an experimental version though, and far from daily driver quality. But Hashcode is on it, so once the custom kernel and all is working, it should have long term CM support.
