I would love to see a true modification or production system, personally i think the BO's skills and captains sould be linked to this, picard wouldn't modify the warp the warp core it was jordi or data. i got a ton of boff's not doing anything but sucking up bandwidth that could be better used for more open sector space.
i think the revamps to alpha centory were week, and the player production was very poorly concieved. the game seems more about the fat loot drops which would trump anything in the R&D tables. the game has turned into some weird evil spawn of WoW and spaceships

. cosmetically the ships look great fuctional simplicity is nice but the deviation between higher tiers and lower tier is rediculous. in fleet battles in the movies and all sizes were used. look at the battle between the feds and the cardasian. miranda class were everywere, as it should be.
I'm gonna go on a limb here but there are a few reasons why a crafting system is not needed in the game.
1) loot drops and ind instance rewards from missions trump manufacturing in the time it takes to build vs. the time it takes to find or earn.
2) along with special currency ie... marks of honor, exploration badges can be gained quicker than it takes to earn them from crafting.
3) the distance / time to gain x amount of materials to produce, out wieghs the benifit.
4) if you haven't noticed everything is nice and tight have a developed manufacturing system does not conform with the overall arcade feel. planets are seconds away you can travel across the universe in 5 minutes. there really is no reason for the transwarps its really not that far away. ground maps are small with finite paths for to follow, there is no nuetral zone.
this game is an el33tist style of video game production, thats why there is huge deviation between ship tiers. i dont like it because it seems boring.
what needs to change nothing, leave STO the way it is an the path its on people love games like this. launch a second server the mirrior universe, few instances few missions and open pvp and fleet area control. that is player driven content. use sector space chase a guy down target the warp engines shoot when you do enough dmg they come out warp the instance is made like a contact. they can build from there