[quote=Zarkun]
Hmmm...the theory is solid, but the execution would be....difficult, since there's roughly ten or so years between the last time we see the NT Warrior and where Geo Stelar and Omega-Xis first wave change. Perhaps run a NET RP that eventually ties in to a later SF RP.
[/quote]

Not necessarily. Not if the setting is about right. 
The events of Battle network take place in 20XX and the events of Star Force in 22XX. Giving this information we can assume that at some point in the span of the 200 or so years they implemented a new system making the previous navi system obsolete. 

Say we run a parallel universe of sorts where we roughly follow the Battle Network and Star Force time line. Keeping this in mind we could say that the lore we know so far exist, however, we'll serve as a sort of inbetween. 

Here me out. It really isn't as complicated as you may think. Now I'm not sure about the official information, but lets say our megaman RP takes place in about 21XX. About halfway between the two series. A brilliant scientist with a team at his and/or her disposal is working on a world wide network of sort that would make the current one almost obsolete. The new EM Wave system (I don't really know and/or remember the system if it was explained, but bleh) is progressing properly. One of our characters could have a bond or relation to someone on the project (for story purposes). We find out that a group of terrorists of sorts are out to take control of the project. Even though we aren't really supposed to, of course, we'll get in the way being the great net battlers we are and such. 

Seem fairly fleshed out and put together Zar? I can try and tie up other loose ends.