I'm a fed player but it's kind of insane that there are 11 non-faction specific ships and only 7 Fleet level Romulan ships, there 14 Klingon specific Fleet level ships and 19 Fleet level Federation ships.
I propose we fill out the Romulan ships and Klingon specific ships to Starfleet's level, a Romulan player should feel like a Romulan commander and a Klingon commander should feel like a Klingon General.
THEN! rebalance the ships, each faction should have at least 1 ships for each role that is the best in that role.
THEN! When we release lock box ships they should have 3 types of ships a Romulan looking one, a Klingon looking one and a Federation looking one.
If you're a Romulan and you get a Klingon ship you can put it up on the market for EC, or recycle it for a small amount of Dil. The same for the other factions.
Disable Visuals on weapons. So a Federation vessel with Disable Visuals on Weapons selected would fire phaser looking energy weapons and Photon Torpedoes. Klingons would get red energy weapons and green projectiles and Romulans would get green energy weapons and light blue projectiles. That way you're not sacrificing looks for min/max.
STF that are more Trek like. An example of a less "Fight those people" STFs would be:
An old alien(your pick which nonfaction alien) starbase is falling into a planet's atmosphere, should it crash into the planet all life will be destroyed.
Escorts have to damage the base to make it fall apart
Science vessels have to help control the fragments that are launching off the starbase and keep people's shields up.
Cruisers have to use their weapons to keep radiation leaks and shrapnel from hitting the other ships while it's being destroyed.(So radiation off the Starbase would be energy weapons and shrapnel would work like projectiles. The person with the highest threat would be targeted just like a normal tactical cube would do in borg stf)
A plasma storm is pushing into a populated system and it needs to be broken up before it hits a small fleet of ships have to disperse it.
The search for a missing ship in the badlands, a group of ships have to deal with the geysers as they go down a corridor where the ship's last known coordinates are.
I'm getting sick of just murdering things. This is Star Trek, it's not just any Sci Fi franchise I hope these suggestions are taken to heart.