The only bad thing I have heard about FMA is if you are flying in an area with alot of hill or nearby mountains, it can throw off the FMA and cause problems. FMA works by sensing the horizon and if it sees hills, high trees ect.. it will fool it.
If you are flying in a flat terrain you should have no problems.
I have heard FMA can even take you from inverted to right side up and strait and level flight.
The other problem you may have is stick input overides FMA, so your computer would have to submit control for it to work.
Do you plan on having manual overide so someone can take over flying in case the computer fails?