Wait what? So we should do what exactly? Stay on 2.3 and simply not update anything at all? I fail to see how having different versions of files creates any sort of rift. It's simple if you want Official Wemade features use Ruby, if you want more Custom features (Stalls, Mir3 Maps, Combo skills etc) then people can use Heroes, and if you want a heavily PvP based Server than 2.3 is probably best for now.
You say Half on Heroes and Half on Ruby as if that's a bad thing. Isn't the whole point of Private Servers to allow people to experience different versions of Mir. I mean otherwise we'd all just play Official. In the end all we're looking for is for Server Creators to give newer files a shot. People like Heroes, people like Ruby, and people also like 2.3. But a lot of people think Heroes and Ruby being newer are harder to create and run a Server. I can't speak for Ruby but Heroes is extremely simple to set up and any issues people have when setting them up are small and easily fixed.
And yes I'd also argue the limitations of 2.3 has been reached. You can only go so far in my opinion with the same Skills, the same Mon AI, and the same features. NPC Scripting can be amazing but it's only one portion of the game.