Sadly, this happened a lot in Star Trek. Someone comes along with a great concept, but it usually gets forgotten and/or abandoned, never to be fully explored. Now, I'm not going to get catty and say "Enterprise as a whole" or "this particular character," I'm going to try to limit myself to specific concepts.
1) Space Boomers (Enterprise) - So, in Enterprise's first season, we were introduced to the concept of the "space boomer." It went like this. Even though warp speed had been invented, it still took many months, even years, for ships to reach other solar systems. (We're talking speeds of warp 1 and 2 and the like.) Because of this, whole generations of humans were being born and raised on cargo ships. I mean, hey, you're on a trip that could take a year and a few months, what else are you gonna do? This generation was dubbed "the space boomers." In fact, the character of Travis Mayweather was a space boomer. Had they developed Mayweather a little more, we may have seen a little more of "space boomer" culture.
2) MACOs (Enterprise) - OK, so Gene Roddenberry always maintained that Starfleet's primary purprose was exploration. That's fine and dandy, but then how the hell did the Federation defend itself? Many a fan has specualted that maybe there's a "Starfleet Marine Corp" that handles most of the Federation's military operations. The closest we ever got to seeing something like this were the MACOs: Military Action Command Operations. As far as we know, they were Earth's army in the 22nd Century. A platoon of them were assigned to the Enterprise to help out with Xindi war at the start of season 3. Sadly, they were not the colonial marines of Aliens. They turned out to be little more than over-glorified redshirts. What a waste. (And yeah, I said I wasn't going to do this, but what would have really helped was if we got to see more of Major Hayes, the commander of Enterprise's MACO platoon. The man didn't even get a first name, for cripes sake!)
3) The Female Caretaker (Voyager) - The Caretaker bring Voyager to the Delta Quadrant. The Caretaker mentions that he had a mate who abandoned him. The Caretaker dies. Captain Janeway cryptically mentions that there's a "female Caretaker" out there, with the power to get them home. That's all in the pilot. We ran into the female Caretaker ONCE, in which she took off and it was hinted that she would return. SHE NEVER DID!! And I always hoped she'd be the Q of Voyager.
4) Voyager's mixed crew - In the first season, they made a big deal of the fact that half the crew was Starfleet and the other half Maquis. By season 2, everyone was buddy-buddy. WHAT THE HELL??
5) The Reconstruction of Bajor (DS9) - It was clearly established that Sisko's primary mission was to oversee the reconstruction of Bajor, with the final goal being Bajor's entrance into the Federation. That was prelevant in season 1. But then, in season 2, exploration of the Gamma Quadrant came to the fore, and then, in season 3, the Dominion War started and all bets were off! Isn't Bajor EVER going to get into the Federation?
6) The Defiant's Cloaking Device (DS9) - The Defiant is the only Federation starship with a cloaking device. It was obtained in a special treaty with the Romulans. The Federation could only use it against the Dominion and the Dominion only, on the condition that the Federation shares all tactical knowledge of the Dominion with the Romulans. The Romulan Empire even went so far as to assign a Romulan officer to the Defiant to monitor the cloaking device. WE ONLY SAW THAT ROMULAN OFFICER ONCE!! This whole treaty was moot after the the cloaking device was introduced.
And that's the start....
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