I wish they would explain what happened to Nanoha at that time IN DETAIL (like an ova or whatever, fuck they have 4 series but can't even make an ova out of the interesting stuff?)
The third movie is supposed to have an original plot and appears to focus on the time between A's and StrikerS; it wouldn't surprise me at all if they chose to explore that off-screen plot arc. That being said, it's a very negative way to end a movie, with Nanoha being severely wounded and facing life in a wheelchair.
They could always end with her recovery. Like they could show the process thru a montage like series of scenes and end off with the recovery. Fairly sure it's been done by quite a few doujins around here but as long as I get happy cute Nanoha and Fate I'm not complaining.