Well, average Swabbie strength is 30, it's not uncommon to end up with half of the starting crew with 40+ Strength... easily the most important stat. The thing you're not going to like is that Throwing skill for swabbies is now 20-60 instead of 40-90; otoh bombs and molotovs are more accurate now to re-balance, so the old crew is going to reap the benefits.
It's strange to hear about micromanagement issues from a Dwarf Fortress modder
Maybe it's not about micromanagement but meaningful micromanagement... Micromanagement isn't fun unless there is something to really manage imo... btw, I've played your Succubus mod for the DF a while ago, it's really cool, even though DF is a nightmare to play (not because FUN, FUN is good, but the interface is beyond horrible). Kudos for trying to add something new and different to the one-colored world of DF (the color being red)
About the research... the tech you've mentioned comes from breaking up Ship Engine research into 3 separate subjects, it normally unlocks power suit (which you already have) and something else, more advanced (in due time).
As for the slave-return - the general mechanic is that any object you research is lost. I could cheat that by making a slave a "living alien" ("slave" object -> research kill -> corpse defined as "slave" object), but it'd mean slaves would take up prison space - they'd have to be way more useful than they are now to go that way, also the whole prison system would have to be redesigned...
The "code" such as $ or S^ is visible in the workshop before the name of a prisoner you're about to enslave, thus indicating what type of slave will be produced.
Another thought, seems that interceptions got too easy with the dodge feature... a single Predator shouldn't really be able to take out a Gunship with starting weaponry
There will be no knee-jerk reactions though, air combat needs more testing.