Deep Space Nine caused a bit of controversy and criticism during it's run, some long-time Star Trek fans claiming it to be 'Anti-Roddenberry', and whilst I wouldn't go that far, I can certainly see their point. Gone is the utopian future established within The Original Series and, to an extent, The Next Generation. Previous Trek Taboo's, such as religion, racism,sexuality and the horrors of war are acknowledged here and dealt with directly, as opposed to being ignored or pushed to the background. The fact is, Gene Roddenberry would probably never fully approved of Deep Space Nine, especially during the show's later seasons, had he been alive during it's run.
And yet this seemingly detrimental statement is why, I think, Deep Space Nine is the best Star Trek ever to grace our screens. Over the course of it's seven season run, The writers of DS9 were never afraid to push the boundaries on what it means to be a Star Trek show, taking risks with storytelling, character and plot. The story primarily focused on the lives of a group of characters living aboard a star-fleet owned station that guarded an ancient, stable wormhole to another sector of the galaxy. It had an excellent cast of characters, each with there own centric-episodes that explored characters and the universe that the show had been established. With Deep Space Nine you never knew what you were going to get - one week you would be treated to an excellent episode that deals with Time Travel in a unique and interesting way, and the next you're dealing with racism in 1960's New York. The show was wonderfully diverse in its storytelling; moments of action, dark brutality and war are complimented by tales of romance, farce and comedy. How about the tongue-in-cheek episode, 'Little Green Men', in which the capitalist-obsessed Ferengi accidently crash-land on earth in Roswell, in the year 1947? Of course, as is the case with any show in which you are tasked to write 25 episodes a season, Deep Space Nine has it's fair share of stinkers. Some of the stand alone episodes are undeniably bad, especially those found in the early seasons. However, the darker turn that the show takes during the Dominion War, and the storytelling that that turn brings - more than makes up for it later down the line.
Ever since it's inception, the show strived to be a different kind of star trek - here we had a space station as opposed to a starship, stationary as opposed to moving. Character's and story-points couldn't simply 'reset' week after week due to the very nature of the show, and this is naturally lead to over-arching plot threads, season-long character development arcs, and a serialized nature of storytelling that had never before been explored in Star Trek.
Ultimately, this is one of the main stand-out factors of Deep Space Nine - the relatively serialized drama made for more compelling watching, at least in my opinion. I use the 'relatively' because although the show did a great job of building up a large amount of continuing plot and story-arcs, and executed them well, as a show it never really strayed away from the tried and tested, 'individual story of the week' structure, which I feel is a shame. Aside from a couple of excellent, 6 + episode story-arcs in the later seasons, the show was still being written primarily as a show that anybody could tune in to having missed a couple of episodes and not feel lost. I feel that if the writers had managed to convince the studio to allow Deep Space Nine to evolve into a fully episodic show, in the vain of Battlestar or Lost, then it would have been even better. I honestly feel this is a missed opportunity, and it is my biggest gripe with the show... Alas, Deep Space Nine is the closest we are probably ever going to get to a serialized drama set within the Star Trek universe.