Battery Recharge Fix will remain of course ..
I'll see about including a mod to keep them if want to use them, kind of depends on how many changes have to make and things and effects it has on other features. Things are often intertwined so may not work.
One issue with the "Engine Expert" ability is I've changed the boats some, to have more realistic acceleration/deceleration times, turning radius, (boats are a little too agile) and dive times. A Gato can now dive when hit the D key at flank speed from surface to periscope depth in 35-40 seconds, which is historically accurate, but before was only possible with the special ability. When I had the engine expert on board while testing new changes, boat will dive in 15-20 seconds lol which is uh not possible for a Gato , Balao, etc. Basically, with my changes the need for the engines expert is not there his is how UBI should have done it, but they were uh lazy and just went the route of special abilities.
Understandable
I am almost finished with this portion of mod, just trying to get few settings correct for fuel usage, hopefully will make it into the release, if not, will have to be patched. Very tedious, time consuming process to get it right.
Torpedo expert will be eliminated. Crew abilities really had no bearing on torpedo performance related to magnetic and duds, they were manufacturing/design issues inherent in torpedo. I've found this ability reduces the malfunction rate for too much, esp after loading a saved game.
Agree. What about Master Torpedoman? I can see that being useful. Crews always trained to load faster.
Medic- I plan to assign the ability to a enlisted man and rename ability as "Pharmacists Mate" , as it is amore appropriate than "medic" for the Navy and the crew member having ability being a officer. All changes work well, will remain.
Never understood why UBI labeled him a "Medic" and an "Ensign". I think "PhM3", Petty Officer 3rd Class should be the lowest rank for him, due to the training involved to become one.
Chief Engineer, like I said it depends. If can eliminate ability to fix everything, but retain the pump speed (which believe can be done as I found in the files settings, havent tested yet though) will keep him, if not, he will go. With the revised (and further revised) damage model , the ability is really not needed and seems to interfere with things Some more testing to do before am sure though.
I kind of like the "Master Engineer" 
Gunnery Special Ability is definitely going, as well as the "Theoretician"
Agree. Kind of useless if you ask me. Just use one of the crew that has a high "gunnery" rating.
"Theoretician"?