Messiah Complex is one of my top 5 favorite X-Stories of all time: just an all-around triumph. Messiah War was a bit of a mixed bag: it had awesome moments (anything involving Apocalypse) and a lot of bloat (anything involving Deadpool). It was kinda fun but mindless. I wasn't crazy about Second Coming at the time it came out, but I think I might enjoy it a bit more upon a second read. It's better than anything we've gotten since, especially Battle of the Atom and IvX, so I guess it's got that going for it.
The unfortunate thing about these stories upon reflection is that Hope's story was fulfilled in AvX, and that's a freaking load. They took what should've been an X-Men story and turned it into a damn Avengers story. It'd be like if you were reading the Kree/Skrull War, seeing the Avengers go through all that toil and strife, only to have the X-Men show up on the last 2 pages, say, "F%&$ you, Avengers. We've got this."
They also never gave any credence to Bishop's claim that Hope killed a million humans: when was this supposed to take place? What the Hell happened?
So much wasted potential, but Messiah Complex is still one of the all-time greats.