The biggest flaw with the A1200 was that it came with a 68ec020 instead of an '030. Maxis quit developing for Amiga after their crappy port of SimCity 2000 couldn't keep up with the Mac version.
I dont think this can be blamed entirely on the hardware, as i heard that running it wihtin a emulated Mac using a Amiga gives better perfomance than the game running natively on the same amiga hardware running the emulator.
So to me it seems like crappy coding/porting is quite a bit of the reason of simcity2000 running so crappy on Amiga hardware.
But yeah, the cpu should indeed have been faster at that time and it should atleast have had more than 2 megs of ram and also a upgraded soundchip.