replacing the internals of the gun with better ones will always result in better performance. Depending on how much power you want out of the gun, you may want to consider getting a reinforced gearbox.
That being said, here are some ideas for upgrades:
For instant trigger response/longevity:
Hi-torque gears
hi-mAh/voltage battery
hi-torque motor
For consistency:
New cylinder head (ARS makes a really good one, but modify and Prometheus can't be beat either)
piston head (ARS, Prometheus and Modify are the only brands you should consider)
Spring guide (ARS makes good ones)
Piston (prometheus HARD piston)
For accuracy:
Prometheus tightbore 6.03 ('nuff said)
Hop-up bucking (ask Amos about this, I can't remember the good brand ones, but i believe that ARS makes REALLY good ones IIRC)
Prometheus (IIRC) metal hop-up chamber
If you plan on shooting a lot in semi, consider buying an upgraded tappet plate and reinforced cut-off lever (This i would strongly recommend).
hope that helps!