Sounds as if in some ways you'll be duplicating a few functions that Wrye Mash already does (activate? esps present) but automating the process more.
FWIW, currently what I do is use a combo of Wrye Mash and Mlox. I put all the mods (BOTH pluginless and those with esp/esm files) that interest me, whether I use them in a specific game, into the "installers" folder WM uses and let WM handle all the file tracking and installation. Then switching to WM's mod tab, toggle the esp/esm I want to use and then use mlox to check load order and conflicts. Works pretty well, especially since WM handles installing and removing the pluginless mods.
The biggest problems I encounter with this procedure is:
1. mods that are zipped in a structure that WM does not recognize. I have to unpack the mod and rearrange it so that WM recognizes it. Then I zip it and put the zip file into installers folder.
2. mods that are released with their own executable to install. Because I've chosen to use WM, I have to do as in item 1.
3. some mods include extras that WM doesn't know what to do with. I pretty much have to work with them on a case by case basis.
Untill I realized WM could handle the pluginless mods, I found working with those frustrating and time consuming.
So, my requests to automate using mods would be
1. a tool hat anolyzes the structure of the mod to make it compatible for use in WM (sorry, I just really like WM now).
2. a tool equivalent to mlox but that handles pluginless mods. As far as I can see, mlox will never pick up on those because they are never recorded in the .ini file. Because WM can handle pluginless mods, I can at least see that type mod in the WM installers tab.
Your point about the bsa files is important. I'm only playing one mod that has a bsa file, but it is easy to overlook when installing a mod. So something that flags those mods to remind and confirm that the accompanying bsa file is actually present and registered is useful.
Whatever you do, keep in mind something to work with pluginless mods. It seems to me the issue isn't installing them but in removing them if one doesn't like the changes they made. I've found WM invaluable if only for that reason.
just my 2 cents
John