I am writing this post, because I think there is something going wrong in Star Trek Online and I would like to share my thoughts on some issues. Some people may agree, while others will totally disagree with the content of this message and they will probably think I am being far too negative. I'd rather call it some healthy criticism.
There are two main issues I would like to discuss here. One has to do with species/enemies in Star Trek Online, the other (which is closely related to the first issue) has to do with the ships flying around in the game.
1) The first issue is also the most irritating if you ask me. To put it simply: Star Trek Online has reduced an universe (or actually: a Milky Way) full of different and interesting species to just a few not-so-interesting species or 'powers'. Just take a look at the Alpha and Beta quadrants: two quadrants once full of different species, have been reduced to two powers: the Klingon Empire (which seems to have absorbed the Gorn, Orions, Nausicaans and a few other species) and the Federation (which also include the Ferengi for a large part). And of course there are some remnants of the Romulans and the Cardassians.
And it does not stop there. Of all the enemies, not a single one of them seems to be a serious threat anymore. Just take a look at the Breen for example. This species used to be very powerful. They managed to attack Earth, destroyed Starfleet Command and were a major opponent during the Dominion War. Now you can destroy several of their fleets in a daily patrol mission, while you are on your own. It is all the same with the Borg: at Wolf 359 there was a fleet of 40 ships. Only one, maybe two of them survived. The battle of sector 001 required a large fleet (and a captain who was disobeying his orders) to stop the Borg. Now they are simply another enemy you can attack when you feel up to it. That's the real problem: once powerful enemies are reduced to easy targets. They don't think (why, for example, is it possible to attack one group of Borg while others keep staring at you during an episode?) and are used far too often.
And they aren't even special anymore. The only reason the Undine were 'invented' in Star Trek Voyager, was because they needed a species who could resist the Borg. In one of the last episodes, Undines are being assimilated. They've just become another meaningless species. The same goes for the Changelings: a species that managed to control several other species, granting them sovereignty over the Gamma Quadrant. They were the brains behind the Dominion War. Now you can defeat them and turn them in for a small amount of Dilithium. Now that is simply ridiculous. All species we have seen until now are being over-used and reduced to something you can get gear or resources from, or fire upon if you want to make an easy kill. I fear the same fate will befall the Iconians when they will get their own episodes.
Of course, in a game like STO you will have to use species as enemies. But instead of a patrol mission containing 5 waves of weak Breen ships, why not put one powerful ship there? Make those Breen a threat again. The same goes for the Borg and the Undine. Make and keep them special enemies, enemies you don't simply defeat on a daily basis. Or, if you have to use them, don't call them Borg or Breen. Call them something different.
2) The seconds issue is closely related to this. I can't take enemy species like the Tholians, Jem'hadar and also the Breen seriously if I see their ships flying around, owned by players. Those Tholians used to be special as well, just like the Breen and all the other species mentioned here. Now their ships are available to Klingons and Feds. This is, just like all the points mentioned above, also reducing the status of those species. So if there will be another lock box, and I guess there will be more, it would be wise to put a better Fed or Klingon ship in it. Say, for example, an Odyssey with a higher turn rate. Or an Escort with some extra tactical console slots. Anything is fine, as long as there won't be put any special ships in those boxes anymore. They, and the species who own those ships should remain special.
(There could be some grammatical errors in this post, as English is not my native language.)
Time marches on and technology improves. The federation with its huge membership has an advantage technically over isolationist empires like those you mentioned. If you want more challenging experiences play on elite settings.
I can sympathize with your dislike of players flying those ships but the way I think about it is that those are diplomatic ships and the player flying it is an ambassador. Lol