There are definitely similarities, but I don't think they're detrimental to anything. There are plenty of differences that distinguish Dark Reign and Siege from those other stories: The Dark Avengers are villains posing as heroes to spin the media against the real heroes, whereas the CSA were actual evil versions of the heroes from another universe. Magneto was just a crafty guy manipulating the Phoenix to act as his weapon in X-Men 3, whereas Osborn is using his own craziness to woo the Sentry into trusting him, and Osborn has in turn been manipulated himself by Loki, Emma Frost, and various others throughout Dark Reign.
So yes, if you simplify the concepts down to a very basic level, there are similarities. But the actual content of the stories are wildly different and, more importantly, they're all fairly entertaining. You don't necessarily have to reinvent the wheel to tell a good story.