Prognosis: Bleak
Partially inspired by chapter 53, I decided to check with a doctor what spending six years in the Gate's environment might do to Al, physically and emotionally. some chapter 53 spoilers ahead (or as much as can be spoiled without actually understanding what they're saying)
By the end of the series, Al will have spent over six years in partial sensory deprivation. He has visual and auditory input, but no tactile input at all. His body is in an environment practically devoid of stimulation.
So what happens after he's restored?
1. Spending formative years (he's been like this since age 10!) in such a stimulation-limited environment could lead to psychosis once he's restored.
2. He might never regain normal tactile input; his brain, so long without any kind of tactile stimuli, would interpret any touch as pain.
3. Though he can 'see', his eyes are not actually doing the work (and there's not much for them to look at inside the gate at all, talk about blankness!), which could lead to problems with his eyesight developing. He might never see the way normal people do, if at all.
4. If his body is not getting any exercise, he could suffer from severe muscle atrophy, and in fact be crippled for life. He'd probably suffer from lethargy and lack of energy. 'Bad shape' doesn't begin to describe it...
5. In chapter 53 we see that he's abnormally thin. After six years of malnutrition, he's probably suffering from some level of kwashiorkor (a form of malnutrition); He might never achieve full height and growth potential, have his IQ decreased, suffer from various skin conditions and decreased immunity.
6. He might suffer from mental retardation, caused (again) by growing in an unstimulating environment.
7. Lengthy sensory deprivation can cause (among others) stress, panic, hallucinations, lack of differentiation between waking and sleeping. The person after being released will also be very susceptible to what they're told, and will have difficulty thinking for themselves.
8. If gravity in the Gate doesn't work the same as it does on Earth...well, that's a whole new kettle of fish, but it's also not good. Think bone weakness, muscle weakness, and lots more.
So what will restored!Al be like?
A semi-paralyzed, retarded, semi-blind, intolerant-of-touch psychopath.
…how wonderful.
How can this be neatly sidestepped (since none of us want him to be like that)?
First of all, there would have to be a definite link between his soul and his brain- his brain would have to be directly involved in processing the information he gets (which it seems it is). His body would have to move sympathetically with the armor, otherwise he wouldn't be getting enough exercise by a long shot.
It's hard to know how much they can feel when they're inside the Gate- the impression I got was that the pain usually kicks in once they're back in the real world. So I dunno how much tactile contact he's getting, which means he might have severe problems with his nervous system (see #2).
It's debatable how severe his malnutrition is, but he's definitely suffering from some. I guess both Elrics will end up on the short side.
Since his sensory deprivation was not so severe, he'd probably get away without the worst effects.
There would probably be mental damage of some sort.
His eyes...well, maybe staring at those Gates all day is enough to save them. Or if he has access to the knowledge inside them, that might also do a lot for stimulation.
According to this, I think it'd be better to just leave him inside the armor....good thing the FMA universe is not really based on science isn't it? *sighs in relief*