I loved the series too, warts and all. But I think it ended appropriately. The conclusion maybe wasn't perfect but it was still satisfying and it did still feel like an ending overall.

I think the big obstacle in terms of expanding its universe into a more modern template is that you don't really have the characters to work with and the characters that are remaining don't necessarily have much significance to support new stories. The best bet you'd have would be a Morpheus prequel story, the trial-and-error of trying to find various "One" candidates, seeds of Morpheus' zeal/fanaticism...etc.

But prequels are just kind of weak to begin with and it only goes so far to playing around in that universe.

Aside from that, you could probably go the 'soft reboot' route and maybe use the Merovingian as a pivot point to tell a story set during an earlier iteration of the matrix. Almost like a Cabin in the Woods approach of a conventional seeming story on the surface but with this additional layer of cyberpunk nerdiness. But it's hard to think of what that story would even be that could make you care about it. Again, at best you come to a sort of "Well it could be about AI that want to be free from the Machine mainframe and live their lives peacefully within the matrix" but that treads pretty heavily on already trodden territory, I think.

The big hurdle, however, is that the Matrix series just doesn't have a lot of good faith anymore. Nor do the Wachowskis. Both are polarizing and while Speed Racer and Cloud Atlas are defensibly great movies, after Jupiter Ascending, they're pretty much toast as far hollywood goes. Meanwhile it's basically become a meme to hate on the Matrix sequels. It'd take a helluva lot of social engineering to pull of a successful 'reboot' or continuation of that franchise I think.