ShamanMick: Yeah, I'm not sold on the clone bay. I think it was primarily added as something to make your boarding actions more dicey, but it doesn't seem worth it to install on your own ship because you really need that skill. Maybe it works well with an all-human ship, so you can just re skill everyone quickly, but I doubt it.
Hacking seemed like a good way of using drone parts. I found that with the Lanius cruiser, hacking the weapons would stop the enemy getting off a quick missile before I could hit the weapons bay, making it through the fight virtually unscathed.
Mind control was hellishly evil. Try using it on the pilot - evasion goes down to 0% and he gets zerged by the other crew.
As for the backup battery, for 30 scrap it seemed a really good investment. It works really well as a way to power systems with long cool downs, rather than having to lock power into them which you can't reroute elsewhere. Combines well with the mind control and hacking.
The backup battery, though I didn't use it much, was pretty much a life-saver those times I did use it. Plus it just makes sense somehow to have a backup battery.
The hacking is cool for delaying weapons fire or trashing drones, but not that great against shields (it's easier to use lasers to take them out IMO). Hacking drones can also be shot down, making it useless against certain ship configs (until the defense drones are dealt with anyway).
The mind control isn't bad. I've used it on enemy boarders once or twice, so they attacked each other instead of my systems. One time my mind-controlled guy managed to win against his buddy, and then conveniently moved to a room right near an airlock... ;)
At the moment I personally hate the clone bay and much prefer the med-bay. I reckon it's purpose is to allow one to take more risks with those events that can insta-kill crew-members, but the fact that it doesn't heal (except when jumping) really means it's only useful for people who don't board. Although I think there are more missile-based "healing" weapons available now (or at least they seem to be more common), which could work well with a clone bay in a boarding config - though I've always hated using those in the past.
BUT...
...the best bit for me is the new weaponry - primarily the new "chaining" laser weapons, the ones that fire faster with each subsequent shot.
There's one in particular which I happened to stumble upon on my first playthrough in AE, around 3rd or 4th sector - it cost 90 scrap I think, and I ended up selling two other weapons just to buy it. I can't remember exactly what it was called - something like "Vindicator" or "Eradicator". It takes five shots to get to its full speed - I think it starts with a 17 cooldown or something - but after five shots it fires so fast, you can leave it on auto-fire and it will burn through ALL SHIELD LAYERS faster than they can be re-raised by a manned shield station!
I had some ships dodging almost every second shot I fired, and it still managed to kill them! MU HA HA HA HA!