No they didn't.
They just removed the optical drive and standard 2.5" drive.
The battery is physically bigger in the rMBP.
And they shaved 1/3 of the thickness as well.
It's physically bigger, but it's not heavier. That's the problem.
I don't know where you got all that from. The throttling thing, the 1.2 GHz thing, the SMC reset, everything seems thrown out of nowhere.
The rMBP has a much better thermal design than all cMBPs and is much harder to make throttle. Unlike the cMBP, Anand couldn't get it to significantly throttle in his review even after running the Half Life 2 benchmark 40 times in a row.
You're right about the bad UI performance being mainly due to software, but the rMBP virtually never throttles and certainly doesn't get stuck at 1.2GHz until a SMC reset.
I got that because I own a rMBP... and mine clearly gets stuck at 1.2GHz until I reset the SMC. Happens under both OSX and Bootcamp after the EFI update that came along with 10.8.2.
The rMBP indeed has better thermals. It's just that Apple is overly afraid of it overheating, so they added unnecessary measures into the firmware to prevent that.
Prior to the EFI update, my rMBP literally zips through everything I throw at it. Now I have to reset SMC every few days, or hours.
It's getting bad enough that I am thinking about bringing it in to an Apple Store. This "issue" is seriously hampering productivity because not only does it lag games, silly things like audio also gets "micro stutter" because of it.