Ok, This bug/suggestions list was long overdue, so it grow to epic proportions. Sorry for the upcoming wall of text, Sleeper, I hope it helps at the end
Bugs:
1. The event with station having satellite system defense going haywire still doesn't allow to leave them alone after "promise to help them". As a result, it doesn't allow to check if you have any blue-event possibilities, without being forced to shot randomly, if you happen to not have any (blue events). (Severity:
Medium)
2. The smuggler that "spin tales of dangers in nebula" - if we fight him and e surrenders, there is no way to try breaking truce with the poor pirate. (Severity:
Medium)
3. Poor helpless refugees that offer various things for trade (or as a thank-you, if we kill pirate using them as bait) seems like perfect target for piracy attempts, but there is no option to pirate them

BTW, in case there is, indeed, other pirate using them as bait, we would still get to fight the pirate, of course. (Severity:
Minor)
4. Both rebel cruisers destroyed on the Federation cruiser special quest (on fed sectors) doesn't delay rebel fleet, like normal cruisers do. It feels a little off, especially after first battle (if we decide to fight cruiser), considering that whole detachment of rebel fleet gets defeated, as result. (Severity:
Medium)
5. Leviathan missile have 2 system damage in it's description, but in fact only does one. I guess that the latter is correct, as only Titan seems like should be able to do 2 system damage (4 hull damage) - otherwise, Leviathan would be much better, with much shorter cooldown. (Severity:
Medium)
6. There are tons of rocket weapons (asteria, all charge - replicating - rocket launchers, etc) that lack engineering option to produce ammo manufacturer. It can really spoil rocketer's day

(Severity:
High)
7. The quest with human crew member leaving (if we let him to) for living with family members doesn't work. Just nothing happens, after our crewman thanks us - no quest location, he doesn't go away, no reward, no nothing. (Severity:
Medium)
8. This engi drone harbor seems to have weapon's placement problem:
http://s3.postimg.org/fo5ced9zn/ring.jpg
After weapon gets activated, it actually moves to where it should be. (Severity:
Minor)
9. There is no way to engineer/produce anything/etc in Hazard Sectors, even on the rare. perfectly peaceful beacons (clear, no hazards) outside of nebulae:
http://s13.postimg.org/4pguwgg8n/hazard_empty.jpg
(Severity:
Major)
10. This poor slug ended in sealed-for-life position

(engine's room) :
http://s13.postimg.org/hkouj7vhz/anomaly_science.jpg
11. I've run into the "Virus" quest - absolutely awesome, kudos! I was really shocked to see that my blue event resulted in totally bad outcome (in fact, wanted to write here that blue events with worse outcomes than white ones is not-so-good idea), just to be totally surprised after fight ended. But, the resulting new crew member was marked as master at two skills, while in reality:
http://s13.postimg.org/vd39eum9j/virus.jpg
No idea if it was intended or not. Also, had other situation, where I was to get Mantis with two advanced (not master) skills, and he ended up having *all* skills at advanced level. (Severity:
Medium or it's a feature).
12. Similar to lacking ammo manuf option for various rockets, boarding drones and many defense variants lack option to allow engineering drone manufacture. May apply to anti-drone drones, too.
13. While the new music introduced by CE is absolutely awesome, the one used in "Industrial" sector is way too loud - much louder than any other music in FTL, new or vanilla one. I think it begs for some normalization to the level of other tracks. (Severity:
Medium)
Suggestions:
1. This event *begs* for blue option if having on-board science lab augment:
http://s13.postimg.org/hkouj7vhz/anomaly_science.jpg
Also, generally, the on-board science lab could allow some other cool stuff in Hazard sectors, following the high risk-high gain scheme. Especially, that in most empty beacons there, you can't do anything else (apart from chatting with crew members), anyway.
2. Advanced FTL navigation - the augment that allows to instantly jump to any previously visited beacon - does it have any blue-event special outcomes? If not, could use some.
3. You might have included it already, but adaptive gel suits could give blue options for certain events, where our crew is pulled into vacuum - like enemy-less plasma storm wreckage beacons, or the one where one of our crew members volunteer to disarm mine and fail. Of course, there are blue-event options that allow to emerge totally on top from those situations, but Adaptive Gel Suits could allow "less" bad outcome - in given examples, we would still get the hull damage, but avoid losing crew member. In the mine-disarming variant, I would also add second stage blue-event requirement of having high level medbay (three?), considering the explosion shock our crewmen suffered. Adaptive Gel Suit could lessen it, but I imagine that she/he would still need immediate high-level medbay treatment. Plasma Storm wreckage field isn't as violent, so I guess only vacuum gel suit would do.
4. We have this possibility of salvaging wreckage on top of Rebel fleet, and certain thing that makes it more safe. I think that Rock's armor plating could also make it safer, but not as much as that "certain" thing mentioned before. Like, 50% worse. After all, ABS barrage *can* get damage-ignored by Rock Plating in normal fight.
5. The fugitive Mantis seeking asylum from Engis have a chance of doing, single-handed, bloody FIVE damage to hull. Really, one damage less than ABS barrage during wreckage-scavenging in top of rebel fleet? I could suspect he can do one or two, destroying two system,s but five? It's really too much. Especially, that in this event, we have chances of getting hull damage no matter what we do (if we give him asylum, he may sabotage ship, if we deny him asylum, he wreaks even more havoc).
Also, some augments (firearms, sedatives, or things like that) could give a blue-event option, where he becomes harmless (in case we decide to trade him for a bounty).
6. Salvaging wreckage on top of Rebel fleet, again - I agree with (and like) the fact that it should be dangerous and not-so-wise thing to do, in most cases. So, the variant where we get 9 damage to hull and gather nothing is OK. But it feels quite strange to hear "you have not been able to even get close to wreckage", if we just killed the enemy crew and have our own people on board. I think, in such case, we should get the "middle" outcome (6 damage to hull, but some resources gathered) as a worse outcome, as our people can just grab nearby materials before teleporting back, no matter what.
7. I understand the thing behind new Effectors, but the older look with 01010110 hacking looked much cooler

(and was easier to notice in heat of action).
Typos:
1. when you get industrial drones ("Sevos") as common trade goods, you hear that "you have no use them" - it lacks 'for', should be "You have no use for them".
Cheers,
/Estel