In terms of quality, none of the stories really stand out for me. Though I will say the Rommie arc is head and shoulders above everything else and really wish it was longer.
That said, I do like how nothing about it takes itself particularly seriously, and you can tell the writers were just having fun. It's like they know the writing is just glorified fan-fiction and they don't care. This is most obvious on how the TCW basically ties into everything.
I'm shooting myself in the foot but I will say I actually think the arc with Worf's son and Torg works as a decent episode of TNG with a tragic ending that actually moved me. I felt Alexander got the shaft in the story but it was a proper end to his story. I also felt the entire Ambassador B'vat arc was crazy awesome and reminded me a bit of how Star Trek WOULD do Star Wars. The Romulan arc leaves me nonplussed but I think that may be because I wrote the original essay which pointed out Admiral T'nae was insane and may have led to it being amended.
Yeah I am also in that camp, I find Online's storylines also to be fan fiction.
It is like "Hey remember that element or reference from the first five series? Well here it is again."
I don't mind expanding on existing material and such and try to give it more context but so far barely any of Online's stuff has worked for me.
Ughh the Temporal Cold War arc, I honestly really wish that Braga had never come up with that plot.
Well, of course it's fan fiction as it's a spin off a popular license produced by fans of the show for its show. However, I'm of the opinion everything after the death of Gene Roddenberry is fan fiction and yet DS9 is my favorite of the series. I do, however, tend to view "Star Trek: Online" as closest as were ever going to get to a "canon" Star Trek sequel as well as something which I view as a natural progression from the original series.
I think I may have a higher opinion of
Star Trek Online because I judged it from the perspective of
Star Trek Online: Path to 2049 which was a World War Z esque collection or tales about what is treated as the most destructive war in the history of the Federation, even more than the Dominion War.
For me, I like the way ST:O "corrected" a lot of what I felt were missteps in the hands of the franchise. Reversing the Borg's Villain Decay (See TV tropes) was a big win for me and I liked seeing them treated as an existential threat to life and the universe once more. I also appreciated the handling of the Undine and my biggest regret of the game is the fact they got shafted in their role as the main villains.
I also felt they handled the Klingon Empire well and my biggest regret of the storyline is the war between the Federation and J'mpok's forces is treated as an afterthought versus what really should have been a central conflict between the two from beginning to end. The Iconians are simply too powerful and alien to make good villains when a better conflict is between two roughly evenly matched powers.
I think the way they handled the Federation is a bit exaggerated but I've always liked how it got a bit darker after the series of disasters which were the events of Wolf 359 to the Dominion War. They've constantly had to test their idealism and make themselves harder until the point we're now officially at a place where Starfleet IS a military organization. Some may not like that but I think it's a fine thing to explore in an MMORPG.
Honestly, I don't play Star Trek Online for the spaceship or ground combat, which can get very tedious and why I dropped the game for five years. Instead, I play the game for the references and the sense of being part of a much larger story even if it's not quite up to the level of Klingon Academy--it's certainly up to the level of Bridge Commander.