It's the same for me. My MR is way quicker than the MT250 I've been working on, and has better throttle response than my RM (less power, obviously). On Tuesday I rode with a guy on a '97 RM250, and was able to keep up just fine. My bike doesn't make anywhere near that much power, but I think we were both putting similar power to the ground in those particular riding conditions (recent rain, occasional mud but otherwise good traction). The RM guy was really impressed.
I think it's mostly the ignition, myself. Adding all that low-rpm ignition advance and pulling the manhole cover off the crank end

really woke the motor up. Porting and pipe work added another huge boost - I have to watch myself in 3rd gear sometimes, when grip is good.
Re the carb richness, replacing the needle jet made all the difference for me, as I've mentioned before. I was running a 115 main / 50 pilot / 3.5 slide with a modified stock pipe, now I'm running a 128 main / 50 pilot / 3.0 slide with a gutted MT125 pipe, and may go to a 48 pilot.
Is one of your MR's a '77 ? The '77 gearbox I'm running now made a big difference in acceleration, and my CR-framed bike will be getting an MT125 box w/MR 5th.
Ray