Honestly, Stargate Atlantis didn't end too badly. It's now on Earth and Earth is a force to be reckoned with finally (SGC's original goal was to acquire new alien technology, and now they have a whole alien city that is cloaked in SF bay). They really just need a new series that merges SG-1 and Atlantis, but I'm guessing most of the actors are a bit too old now (hence, the mess that was Universe, but I still enjoyed it despite its teenage love-triangle bullshit). The two that I wish had endings were: Dollhouse, which got really amazing right at the end but never really finished (a Joss Whedon production, check it out!). The second one was that they tried to remake that old 70s show called Battlestar Galactica in 2003. They had a 2 episode miniseries that rocked and then they didn't get picked up for a TV show unfortunately. It could have been amazing.
It had a sort of ending but they left too many plot points up in the air, and it was a rushed conclusion since they thought they had more time. The movie, Extinction, was going to be basically Atlantis going back to Pegasus and had some sort of plot involving ending the Wraith for good. It just felt like there was so much more they could have done. There's a series of post Atlantis novels that are still being released, but I haven't made the jump yet to reading EU stuff for any franchises really. It's on my to do list though. Haha I'm guessing that you didn't like the end of BSG. I didn't mind it, but I did think ghost Starbuck made no sense.
Ghost Starbuck made no sense. Them sending their ships into the sun made no sense (now they are less likely to survive). The fact that they found a planet that has the same constellations as our Earth light-years away from our Earth was the thing that got me. If the constellations were to be the perfect guide for them to find their Earth (I imagine they could be relatively similar for some planets) means that if there was one planet that was light-years away with the same constellations as our Earth, then their little quest to find this map to the real Earth would have been pointless because they would have known it wouldn't narrow down a planet like an address. The only thing that made sense was Cavill committing suicide, and that was improvised on set. For a show that entirely existed as "just wait! we have answers at the end!", the end was awful. I got tricked by Alias and BSG, but thankfully I stopped watching Lost after one season because I saw that it was going to be the same thing as Alias. I will never watch a show again that is "just wait! we have an end that will blow your socks off!".