Agreed on all fronts. I'm almost always on the side of having a new character exist alongside an old character, rather than outright replacement. Even in cases like Cho and Jane Foster, where I find the "replacement" character more interesting than the original, I'd still rather just have both. It's a win-win.
Back to the Clone Saga, even if they had just had it so that the Peter we had been reading about was the real Peter, but was replaced by Ben once Ben returned, that would have gone over so much better. There would have been backlash but not the hate and hurt that came from hearing "the Peter you know isn't the real Peter". That MIGHT have worked. But the combo of "your Peter is a clone" and "he's going away anyway" was too much.