I don't think you have to throw it out. Just continue onward from where MMBN6's ending left off with Netto/Lan growing up after 20+ years, marrying his longtime girlfriend and having a son who was poised to take over where he left off, along with his own Navi of "Rockman Junior". And then we can do pretty much the same things over again, only this time with most of the "classic cast" grown up, having kids of their own and etc. Have some new nefarious net-terrorist cell arise from the ashes of WWW to cause trouble. Have a few more "MMX-isms" in the mix for fanservice appeal. (As if Zero, Colonel and Iris weren't already a sign that things could go that way.) It doesn't have to be difficult~!
The thing that would make that angle work so well, in my opinion, is that you'd be able to create a world that marched with the procession of technology in a believable manner to our current frame of reference, much like MMBN did for the 2000s. The last EXE game came out nearly ten years ago. A lot has changed since then, and I'd like to see just how much that world changed too (forgetting Ryuusei/StarForce exists, at least).