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I think for the most part, the writing is quite good in STO. There are better missions, and worse missions, but in general the Fed storyline feels like star trek.
If you want some details/explanations:
The Klingon front in particular has very good story arcs. It deals with weapons of mass destruction, genetic manipulation, etc. There are several cases there where the players see disagreements in the Klingon Empire about what constitutes an honorable fight. It also closes some loose ends (in particular, the popular "TOS human-like Klingons vs. TNG Klingons" in-universe lore).
The Romulan front shows some lore about the Hobus super-nova and plants seeds for the Iconian back story, which shows up every now and then. The Cardassian front shows what happened with the mirror universe after they got the Defiant-like "warship", Cardassia's dealing with Bajor and the true-way, and even an encounter with the prophets. Oh, and there's that tribble episode, and the section 31 episode where the player has a choice of believing a Starfleet Captain or a Section 31 Agent.
The Undine front is also very nice - showing true Starfleet values of pursuing a diplomatic solution of mutual understanding instead of just firing at every Undine on sight.
The FE are even better in this stuff:
The Devidians - moral dilemmas about Section 31 and dealing with extreme threats to the quadrant (like several episodes of DS9) and preserving the timeline (accolade for not hurting anyone + ships disabled and not destroyed + failure if one kills the KDF ship at the end of the series). Also, a nice twist in What Lies Beneath, the slingshot time travel, meeting Scotty and Bones in the past, and several other lore stuff.
The Remans - dealing with slavery and independence, weapons of mass destruction (does the end justify the means?), etc. The player even has a choice whether to aid Obisek or try to arrest him.
The Breen/Deferi - starfleet coming to aid a pacifist race, while pursuing ancient knowledge in a mystery/puzzle-sloving action? seems as TNG as you can get.
I have many more examples of very very good writing in STO, but I think this post is long enough to make my point. As for the Foundry - just try City of the Polmar Ree and Spirits of Ramok Nor, and then tell me if you see "bad writing" there...
EDIT: Sorry all. This thread has so many reported posts coming from it that I can't let it go on any further.