@ clear_lot:-
Dual GPU should be seen in the context of getting a card today, and adding another one a year or more later to increase the value of your existing card. And in CF, cards can be used of different speeds and shaders etc. and they will perform at their max possible level without lowering down. Only exception afaik is VRAM, which will be the lowest of the two cards.
What you say about microstutter is correct. Toms Hardware has a detailed analysis here and recommend 6950 and above for CF:-
Micro-Stuttering And GPU Scaling In CrossFire And SLI : Micro-Stuttering, Multi-Card Scaling, And More!
However, Cilus runs 6870 CF and has not reported any problems regarding microstutter so far.
And for AMD boards, they support more PCI-e lanes for 990fx chipsets than Intel's 1156/1155 based boards, so no issues on that front. For dual GPUs, you are going to get x16/x16 in most 990FX boards.
Driver support for CF for newly released games is still not up to the mark if you ask me. So if you are in a habit of playing games on the day of the release, this may be a matter of concern. But then, if you are really in a habit of playing games on their release date, you should be able to take care of drivers, disabling CF if necessary and other nuances of dual GPU setup.