Drone controls aren't man-able either, but there's nothing that manning them could give you anyway. Well maybe they could have made the drone rebuild faster if manned?

Cloaking, hacking and mind-control also aren't man-able, which is a shame as it would have been cool to decrease the cooldown of these systems by manning it and/or increase the duration of their effect.

Actually I think I changed my mind a bit on the "charge" weapons. They're slightly annoying to use, but they do provide a significant level of flexibility. For example, if the enemy has full shields, then go for full charge, but if they're down then just fire single shots to damage their systems quicker.

One thing about the backup battery I don't see people mentioned yet: it makes getting the Zoltan Ship achievement "Get to sector 5 without ever upgrading your reactor" a lot more easier. Every time a battle would start, I would use it to power up a couple more of my weapons: therefor didn't have to resort to a plain laser.

Maybe for drones the drones could all get like +15 hitpoints, +10% movement for bots since they are being controlled to be more effective, and get repaired faster. Perhaps the 'hull repair' could go for a 4th repair cycle rather than just 3.

Cloaking, manning it would probably help reduce the penalties of non-cloaked weapons, dropping say 15% of the lost cloaking time. hacking and mind control, haven't seen/touched those so I don't know what to think.

Manning the O2 should give an addition 1x multiplier on speed for filling the ship (you're changing out filters and stuff, maybe controlling air flow to go more into certain areas that need it).

Thanks. So long as it gives you something that you can put your guys to work for a short advantage.

As for 'ultimate' I doubt it. Maybe something a little more low key, like 'Super Mega Extra Enhanced Advanced Version!'.... or SMEEAV for short :P