Surely the most contemporary example must be of the character "Rachel Dawes" from the Batman trilogy. They got Maggie Gyllenhall to replace "whats her face" :)
Spiderman - Andrew Garfield in - Toby Maguire out
The incredible hulk - Mark Ruffalo in - Edward Norton out

The rebooting of Star Trek is still a controversial topic among trekkies, especially the older ones who grew up with the original 60s show. I would imagine this kind of thing feeling like being a Beatles fan, and some record execs putting a band together nowadays called 'the Beatles'. It's just not going to work for people who are invested in a certain franchise.

The best example I can think of is the Hammer Dracula series with Christopher Lee. Apparently Lee hated working on the sequels to the 1959 Dracula, and he only did so out of pity for the studio, which were losing money at the time if I'm not mistaken. However even when Lee did leave once and for all, Hammer still released some sequels, such as Brides of Dracula and Legend of the 7 Golden Vampires, which, let's just say, weren't the best films in the series, and that's saying a lot.

X Men 3 ... where the hell were Bryan Singer's X Men hiding?

Friday the 13th Part 5 – A New Beginning: Instead of Jason Voorhees, the film has a copycat killer pretending to be him. To say it’s a bad film is kind of redundant, as they’re all terrible. Yes, even the first one.