I think what the Matrix had going for it was it did manipulate audiences in a good way. The same way Hitchcock didn't let audiences know what Psycho was about going in. You go in expecting one thing and by 1/3 through the movie you are completely blindsided.
The difference is Psycho is a masterpiece worth rewatching in minute detail for its brilliance. After the initial surprise of the first viewing or two of The Matrix what is left is an action movie that is damn good but pretends to be more than it is.
Not the best of its genre in the last 25 years, that's for damn sure. It was innovative in technology and special effects but after the first time through and the surprise is gone you are left with a movie that is good, but too shallow and pretentious to be as great as its fans declare it.
And yes, I would say Serenity is the better movie. Hands down. Not to mention Blade Runner, Children of Men, Terminator 2, Aliens, Minority Report, etc. etc.