The 2000 is my favorite but I'm biased, it was my first computer and I have a bunch of expansions for it already.
You can find accelerators, RTG cards, networking, and so on, for either one. The 1200 has a couple advantages - new things are still being developed for it, so what's available uses newer tech. A lot of it requires converting the thing to a tower case, though.
What's the best solution? If cost is no object, get a 4000, 060+PPC, a PCI busboard, some fancy graphics card, and so on. If cost is a limiting factor (and when isn't it?) then you need to just look at what you can find for both and evaluate how much you're willing to spend.
As far as AGA goes, if you expand the A2k and still need AGA for games and such, keep the A1200 around just for that (maybe with a RAM expansion, as mentioned earlier).
-Jupo
