I see your point about why you would want it to be official (as in: merged with the mainline mod) because you want to ensure that two current versions of EB 1.2 are both compatible with each other and include the alterations required.
But this needs not neccesarily be the case. First of all it requires basically cutting a faction from MP. Maybe OK for you, maybe not for others [it may be their favourite faction wich draws the short straw]. The obvious candidates (Hellenic factions because there are relatively many of them) are all subtly different in their faction line up, something which is more pronounced in MP.
Let me illustrate the point: an MP battle is, I'd say, about pitting two exciting and capable armies with a real human commander so there is a challenge for the human on either side and a little feast for the eye (pitting one standard and a bit dull army against another would take out quite a bit of fun, would it not?). And the exicting, feast for the eye stuff is where all those factions are quite different. AS and Makedonia do have a different roster. Ptolemaioi and AS aren't copycats (quite a different line up in the elite units there). Makedonia and Ptolemaioi aren't created equal. Epeiros and Makedonia are different from each other too. One would expect a player choosing Makedonia to field a distinctly different army from a player choosing any other Hellenic faction. It really would be like cutting a truly unique faction for the sake of introducing a boring clone faction.
Second of all, and this is much more important perhaps to you: the thechnical considerations are hollow. If you take the time to do design this mini mod properly you can easily see the rather obvious solution to `compatibility'. Be clear about what mini mod you have, specify it when you challenge opponents. That is what any MP player is used to, and should do, anyway. And on the part of the minimod creator: include a map.rwm file with your minimod. You may want to explicitly require people to have the trivial script installed, so they can automatically patch their game back and forth between whatever heavily modified single player set up they have and your own MP only minimod.
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