First of all, let me buck the trend and state that a) I don't think that Brett Ratner ruined the X-Men franchise with his work on this, the third movie in the series; and b) whatever's wrong with X-Men: The Last Stand - and there is plenty - isn't all Ratner's fault.
In some respects, the revered-in-his-absence director of the first two installments, Bryan Singer, laid a lot of booby traps in the storyline that even a gifted filmmaker - which Ratner is not - would have a hard time fixing. So much of it comes down to Singer's original hit-and-miss cast, and how they fare in X3 depends on how the individual actors fared in their careers over the last six years. For example, Hugh Jackman proved to be a successful star as well as perfect in the fan-favored role of Wolverine, so it's no surprise that he should take the lead in the film, even if it messes up the traditional relationships set forth in the comics. Unfortunately, Halle Berry won an Oscar somewhere in between her bland turns as Storm, and so she is also given more screen time in a role that, to be fair, was never well-developed in the first two X-Men movies.
Then there's the issue with Cyclops.
It was clear early on that neither Singer nor his screenwriters liked the character much - even though in the comics he is the leader of the X-Men and has his own interesting story to tell - so Singer cast a weak actor (James Marsden) in the role, then gave him little to do. Thus when Cyclops is rather casually "let go of" in this movie, it was probably an inevitable filmmaking decision (it should be noted that Marsden also left to work in Singer's Superman Returns), but his abrupt dismissal from the X-Men saga didn't please me in the least as a childhood fan of the comics. That this also happens during a key scene - the rebirth of Jean Grey, aka Phoenix - shows that Ratner has totally dropped the ball. In a moment that should be chilling and awe-inspiring, it comes off as flat, rushed, and strangely uneventful.
Still, the movie's not as terrible as the fanboys would have you believe. While the dialogue is goofy and cliche-ridden (the characters keep overstating the obvious throughout the film, e.g., somebody returns and then somebody else says "You're back"), I almost accept it as an homage to Chris Claremont's corny banter from the "golden age" of the X-Men comics which he wrote in the '70s. But overall, the story is good; while there are lots of missed opportunities in the details, the dark and scary Phoenix plot line hits most of its marks, and Famke Janssen (who waited six years for her chance to cut loose) is quite effective in the role. Even Kelsey Grammer, an unlikely choice to play Beast, is a surprisingly welcome presence.
The film itself is mostly a series of action scenes and special effects that have little magic to them. Pardon the pun, but I agree that Bryan Singer brought some sort of "X factor" to the first two films. He's not a great filmmaker, but there was a grace and imagination in those movies that isn't here now. X3 is little more than a standard Hollywood action picture that, while it does gain some emotional resonance during its grand finale, still feels like a chunky work in progress in need of some extra detailing.
And by the way, what happened to Nightcrawler?