I don't plan to make a plugin for each expansion because the official patches fix some things and I'm not sure you can apply the later patches without the expansions with no problems. The later games also use the same version number whether there is an expansion installed or not, so I assume there is some difference in how it all works together. I've only ever had the GOTY versoin of MW, so maybe someone else can say more about this. I did try patching just MW once to test something, but there were some problems since it couldn't find the expansion .bsas
In any case, I'm not going to reimplement fixes that are already there, not to mention it's a lot of work for little benefit. Modulating each .esm would be very messy too. I'm sure there are still people out there without the expansions, but just about everything going on for Morrowind these days requires the latest version/expansions (most importantly, the MCP) and GOTY is cheap. Ideally, I'd like to fix the .esms themselves or merge them, but I doubt that would be easily adopted.
I might end up doing something for the official mods. There is a patch mod for them already, but it does more than it needs to in my opinion. As for why it's an .esm, it's to ensure it loads before regular mods. The unofficial patches for the other games are .esms too as far as I remember.
No, it's just a setting change in the spell's properties. Gameplay > Magic Effects > Base Cost.
Just as you stated, a plugin for quests/dialog, one for scripts, one poorly placed objects, etc. Modular meaning broken up into smaller modules. Although deciding where to break up some things is an issue due to things overlapping, like scripts for quests, for example.