I want a total new approach.
reset the era to the loast era (post TMP-pre-TNG)
drop the whole class deal (engineer, tactical, medical) and inster a skills based system. use char creation templests, but don't resrict players to a "class" path.
drop the Starfleet only aspect. put in 3 factions, let players choose what Faction theywant to align themselves with. I'd say Fed, Klinks and Rommies to start with, others could be added in expansions.
Also on that token, allow players to play a civilain path, explorers, merchants, ect
Ships: should have interiors for the most common places, allow players to interact with the ship, repairs, replicators, shuttle bays, ect. also ships should be fully destroyable, making players really dedicated to preserving it. Ships also should require fuel and supplies. want to go warp 9.99 around the place, fine, but realize you'll burn up fuel and have to use fleet points to replenish it.
Space: vast, make sector big, use warp scale in them and make players take more than 2 seconds to go from earth to Romulus. on that token, make some sort of fast warp system to get from sector to sector, i don't think many players would enjoy the 3 month journey from one side of fed space to the other very much.
Player run economy (yes i know the feds don't use cash), in which players make goods, transport and distrubute them for either their Faction, or as independent mechants for profit. and we all know around the LOst era, there were still soem fed citizenxs with greed.
that's my short list for now......