Can't wait for your overhaul.
As an atmos tech, it is vital for scanning canisters so you can tell what gas is inside them. One thing I wouldn't mind is being able to take records of scanned canisters, what it looked like, what was inside, ect ect.
Flashlight is always helpful.
Messenger gets a bit of use, it would be great to have it combined with the crew manifest (finding people on high pop is a nightmare) and allow for multiperson conversations.
Some kind of chatroom would also be fun.
Cart system is good and rather interesting, I don't really see a reason to just remove it. Haven't ever removed/replaced a cart though.
PDAs fit perfectly into the SS13...."theme" of everything being an unlogical mess! They are both completely outdated yet magically powerful.
No idea what a potato uplink is.