First off, the only worthy replacement of a mian character was when Kyle Raynor replaced Hal Jordan as Green Lantern...simply because he didn't try to be Hal Jordan...and he wasn't supposed to be. He was an entirely new character, and his being a Green Lantern was okay because there has always been more than one.
Ben Reilly was a CLONE of Peter. He was an inferior little test-tube-Peter-Parker, and that's it. He was brought in to replace the ONLY REAL Spider-Man (aside from Miguel O'Hara, who ruled). That was his only purpose. When you tell the readers that the past 15-20 years of stories they've read have been about a generic version of their hero, they're going to get pissy about it, and you can't blame them.
The "Peter was the clone all along" thing was a screw-up of gargantuan proportions. If they wanted to replace Peter, they should have brought in some completely unknown character into the mix to do so, as opposed to reviving a long-dead and oft-forgotten character to replace a hero alot of fans had put a great financial and emotional investment into.
Also, writing Peter out of it all and having "Ben" take over was just a disaster all along. Peter was still around, and we knew he would come back eventually. That's why they didn't just write out Ben. They killed him....3 times. He was stabbed through the back with a Goblin Glider (fatal), Dropped 50 stories (fatal), and he disintegrated into dust (FATAL). For all those who want to give me the "perfect clones don't disintegrate" bull-s***, I offer this: HE WAS DEAD. HE RETURNED TO HIS BASE ELEMENTS AT A GREATER RATE OF DECOMPSITION THAN A NORMAL HUMAN BECAUSE HE WAS A HOME-GROWN HUMAN. So eat it.
Now, I know BR had some fans, and that's cool. Then again, Cyborg Superman and NFL Superpro have fans out there as well. It's not called "The Amazing Spider-Clone" or "The Amazing Spider-Exile", it's "The Amazing Spider-Man".