I have both. My A1200 always has been my main Amiga, but my A2000 is closing in, hardware wise.
The A1200 had two advantages the A2000 has not: AGA & 32 bit.
Th A2000 has two advantages the A1200 has not: built in expandability and easily replacable chips.
In both cases, you can more or less work around it: with a nice turboboard and an RTG-card, you have a very nice A2000, while you can put the A1200 in a tower to improve expandability.
In the end, they are both great systems and I don't prefer one or the other.