Whip, you keep bringing this up. Don't you realize that they will most-likely always be incompatible. There are too many major differences: trade routes, superweapons, flak/carriers, not to mention starbases. How would a vanilla player fare against an Entrenchment player that could deploy starbases? Impossible.
Perhaps there would be a way to seamlessly see both types of game and join either by activating or deactivating the expansions.
I just want to say that I really like Sins but Sins handles multiplayer, updates and mods VERY poorly. I don't know technically why that is, but it is very off putting. Many other games have updates but they don't wipeout game saves or require a complete rework of mods and maps. How long has ForgeTools v3 been out and yet if you try to make a mod with the reference data given, you will fail. This hasn't been fixed yet?!? Sure you can work around it if you're REALLY interested but you have to wonder how many new people have tried using the tools as is and gave up when they failed to make a mod work.
Sorry my 2 cents. Sins is great and I know Ironclad has worked very hard on it. That's all I'm going to post on the topic. I'm not interested in an argument about why or why not.