On the new server, we could make refits more customizable and novel. Like a K-D7 with +1 APR for 40 total power. This ship would not exist in any player's static shiplist. It would exist only on the server. This is a subjective can of worms to pop open though.
We can give better or worse quality officers to the AI and to players, instead of every officer in the campaign being junior. The game mechanics do change when a legendary officer is present in SFCOP! We simply never saw this in EAW/OP (outside of SFC:CE, briefly) because the default officer grants neither a bonus nor a penalty. Green officers really are poor. And legendary officers are very effective. If every player has a LWO, then that concept of rarity is broken. The new server can limit the availability of legendary officers, through an officer "shipyard". But this is a level of micromanagement. Some players may not want to go through the tediousness of searching for and recruiting officers. Just assign them randomly at 1%(legendary), 19%(veteran), 40%(senior), 40%(junior), 0%(no rookies) or similar.
Obviously many of us didn't care for SFC3's "pimp-my-ride" approach, and we preferred navies with standard refits and very limited customization (e.g. missile load out: TypeI or TypeIV, slow/med/fast). But the SFC1 refit and officer systems were not too bad.