Well unfortunately its well known that not even the Fans can clearly agree on what is good and what is bad.
Eventhough that may be true for the details I think that fans seem to agree on certain very basic issues: No WoW-Clone, no grind heavy game play, strong emphasis on team aspects, no dumded down "iconic" class or skill system and a more complex and meaningfull crafting system then in most MMORPGs, to just name a few.
EDIT: Oh, and PSIs. I guess at least eighty percent of the fans agree on PSIs being needed. The debate was basicly about PSIs at launch or PSIs as Add-On.
Where fans are mostly disagreeing on are, in my experience, questions about design issues as uniforms, ships, graphics (realism vs. cartoonish) or what timeline the game should be set in.
And then there are some questions inbetween, that for the most part are disagreed on due to misunderstandings and misinterpretations: Money or Prestige, trade, loot, etc.
The misinterpretation is mostly, that the people who do not want money or loot in the game propose systems that give all this things different names and slightly different designs, while they basicly still serve the same purposes. Some people just dont read all that proposals carefull enough and take headlines like "No Loot" all to literally.
That the fans make the impression as if they are totally devided in there oppinions has more to do with the passion and that debates easily get very heated by this. Taking a close look at all the debates shows that the fans are not half as devided as it seems on first sight. Its just so that Star Trek fans have a tendency for desperation and eagerness, the evil twinbrother of passion. The way the Star Trek franchise has gone the last decade plays an important role in that.
