I was apprehensive but the movie turned out to be very good. It does play around with the characters' histories a bit but nothing too offensive. Marvel has always played it a bit loose with character ages but I think Storm, Cyclops, and Jean in X1 were meant to be a fair bit older than their comic versions. If Storm was alive in '62 then she would be 40+ in X1. Thus, making Havok 10 years older than the version of Scott we see really isn't a terrible stretch. Gambit must be quite old too following his appearance in Wolverine.
I felt that the Beast had a nice, self-enclosed arc in X3 to the point where they wouldn't need to use him again, so using him in the prequel worked really well. Nightcrawler's story clearly isn't done though considering their choice of characters in the prequel. Banshee and Havok's training was handled well.
Moira was the strangest one for me. It looked like her part was written for Carol Danvers and then at the last minute they bunged in Moira instead. Of all of them, she has definitely aged the best in X3, unless you include Emma Frost, who seemed about ten years younger in Wolverine... If the use Emma again I'm sure they will hand wave away the fact that she should be about sixty. If they don't, I really hope she starts to moderate her outfits...
I'd still prefer to see X4 (I'd hate to see classic plots ending up in the past) but I admit that the prequel franchise has legs too.