Aside from the what really matters (story, character, relevance), my geek list includes:
Bumpy vs. Flathead Klingon bigotry with one subjugating the other due to the flathead's more human sensibilities, possibly leading to ethnic cleansing civil war. Extensive development on their history and culture and a look at their industry.
Remans ( as oppressed species metaphor but also deadly antagonists ) - The only thing I liked about Nemesis.
Ferengi - after cursing their creation on TNG, DS9 made me love these goofy little basterds. They represent the current state of humanity. Possible stories about how they got ahead by buying tech, elevating their culture through acquisition rather an invention and the problems that can cause.
A better sense of scale in depiction of large ships, cities, etc. Limitations of time, tech, and budget made many old sets look more like stage sets than theatrical ones.
At least one seriously flawed starfleet officer (looking at you, Garth) - Someone who damages starfleet's rep and credibility, etc.
No antagonists that are way out of their league - I love Q, I really love the Borg, but they have no place right now.
Compelling dialogue - This is where the medium of TV shines, and Trek could do better here. Techno babble should not go completely, but should be tempered and weaved into the dialogue more organically.
No humanoid looking androids - It was painful to watch Data age. He was awesome but that won't fly these days. More mech-like automatons would also help give a retro feel while being cool with the young people, but not droids.
When continuity works, pay homage. When it doesn't, eject it - Data's origin was terrible, and when he became a standout character they were forced to develop it even more. I couldn't help thinking that Soongh in season 3 could have easily retconned all up to that point.
