My only problem with the way the series ended was having just about all the main characters leaving for some super-important new role- Federation Ambassador to the Klingon Empire, Grand Nagus of the Ferengi, Chancellor to the Klingon Empire, Savior to the Founders, etc... It was stretches things a bit when the cast are giving pivotal roles in major events, like Sisko being in charge of the Alpha Quadrant Assault.
I do like how they did tie up all the plot threads, but I wish they did not feel obligated to give everyone a special send off to greater things. "All Good Things" got it right- you saw the command crew together, having finished a big adventure, the ship moving off to new missions which we just never saw. I like the idea of watching events unfold and having the feeling things will continue afterwards as before, we are just not around to see them.