That was similar to my take on it: Reloaded & Revolutions should have just been one movie with a few less (or shorter) action scenes.  There was just enough plot for a LONG movie, but when you stretch it between two movies, it becomes obvious that they either 1) had too many ideas for action sequences to fit into 1 movie or 2) really wanted to make double the money.  Probably a bit of both.
My personal preference would have been shorter sequences... a good example is the "Agent Smiths" scene.  They should have built the numbers up more quickly.  Why?  Assume you're Neo for a sec.  You're pounding on Smith, but can't seem to hurt him.  Then another appears, then another, etc.  How long before you just run away because all you can do is throw them around, but aren't hurting them?  Not as long as it takes in the movie, thats for sure!  They could have gotten the same effect by just upping the Smiths quicker, still had cool fight scenes, without me thinking half-way through "Fly you moronic toad, fly!"
Just my opinion, I know there are people that loved every second of the movie, but I think it was a decent story diluted by the many lengthy action sequences (and that lengthy dance/sex scene from Zion).  It just seemed like I was in "bullet time" while I was watching most of the movie!