Some thoughts:
I played MXO from a few months after its launch until the very end. I want nothing more than the virtual life I led there, the decisions I made, the battles I fought, the sacrifices and indeed the mistakes I made towards advancing that story to remain canon. But fewer than 300 people were playing by the end. If it remains canon, I'll be astonished. Pleased beyond belief, but astonished.
As for dead characters: Neo's fate was ambiguous. The Machines never returned his body to Zion. There was some evidence to suggest he might have been returned to the pods and given a new identity as a woman named Sarah Edmontons ("I thought you were a guy. That was a long time ago..."). Morpheus got himself killed, but there was always evidence that he might have faked his death. He seemed to return at one point, but it was actually an impostor program created by an exile for the purposes of disrupting peace. It thought it was the real Morpheus for a while though. Also, at one point The Machines made a duplicate Morpheus program for some stupid-ass reason I can't remember. Trinity came back. It's a very long story, and one that was never resolved before they pulled the plug. But long story short: she was a program the whole time, inside a human body, but didn't know it at the time. I loved MXO to death, but some of the plot threads were not great. Smith was never -completely- destroyed by Neo. He'd resurface from time to time in a weakened form. Agent Gray was known to exhibit Smith-like outbursts from time to time, implying that a little bit of the infection lived on in him, but he remained loyal to the System. The Oracle got herself killed, but she quite literally saw it coming, and was implied to eventually be able to return in a third shell.
Also, the Truce between Zion and the Machines dissolved about two years or so after it began. Both sides took liberties with the conditions of the peace, but the Architect was the one to call it off... though, it turns out, there were other players pulling the strings of the Machines themselves. This part is very hazy, and the least resolved of the unresolved material. But a story outline posted by the final writer before shutdown indicated that there would ultimately have been a new peace.
Point is, there's ample room to bring back anyone, and have the story play out in any sort of backdrop they want, regardless of whether they toss MXO into the same hole as Star Wars Legends.
If nothing else. I'm just happy to see one of my favorite fictional worlds again! It's been 10 years since MXO shut down, and there hasn't been a day that I haven't missed it.
And at the very least. I can continue Robots VS Kung Fu for years to come! I now have ideas that can take this thing through at least a part 5, maybe further, depending on what I'll have to work with when the new one's released. As soon as I get over this tinnitus and start sleeping again... I have a lot of work to catch up on!