The Matrix as a concept, world, and overall setting definitely has the potential for more (worthwhile) stories. Isn't Neo like the sixth One? That's five prior "versions," of the Matrix that you could pull entirely different characters and locations from. Make a film (or two, fuck it) of The Animatrix's Second Renaissance - I'm picturing like Terminator: Salvation but written with more depth and emergent ideas for the viewer.
Make a movie in the interim between 3 and 4, use the best elements from the story of The Matrix: Online and have a good writer build a compelling narrative around it. Make a movie about Exiles - could be Merovingian related or completely separate, but it's good grounds for a protagonist with "powers," who isn't framed in the same messiah archetype The Matrix is so fond of.
I'm not even saying another film or three with Neo and...Trinity (was gonna say the original cast, but that's basically all there is in the canon of 4), just CRAFT IT LIKE YOU AREN'T STUFFING A HIGHSCHOOL ESSAY WITH BULLSHIT TO MEET A WORD COUNT.