I actually really like the 3 Matrix films. The 2nd and 3rd deal with much more heady themes, and thus are panned by the vox populi who only want to see bullet time fights in the Matrix, and not the grim reality of Zion.
The only thing that doesn't hold up, actually, are some of the CGI effects. The Wachowskis pioneered some stuff in the original, and then tried to be on the cutting edge of CGI, and it ended up looking rubbery. CF the Burly Brawl with Neo and the dozens of Agent Smiths, where his coat looks like a rubber sheet waving in the wind than actual cloth.