I realize that I'm skipping through parts of your post, but I'm just commenting on what I know. The rest will need to be addressed by someone else.
- For archives that are not BAIN-ready, all folders that are determined to be under Data but are not known folders like Textures or Meshes should be displayed as packages. I think this would cover a lot of archives that otherwise need to be converted for BAIN.
This (and similar ideas) has come up before, and Wrye was against it. The main point that he brought up is that an archive should either be BAIN friendly or not. If BAIN recognizes the format, it will install. If it will install, it will work. BAIN shouldn't try and guess how to install a package. If it does, then it might install, but not work. Or, it might work. The problem is that there are then no guarantees. There's simply too much room for error.
The current specifications for a BAIN friendly archive are pretty broad, and allow a wide range of possible installations. I'd be extremely hesitant to change it at this point.
Other changes I'd like to see in Bash:
- More flexible values for Tweak Settings, preferably an option to manually enter a value. In other words I'd like an option to set the death timer to zero seconds, whereas right now the minimum is 15.
Agreed. This would be nice, but also require a UI change. Not sure how much work would be involved since I mostly worked on the back-end.
- Some way to relocate the files Bash places in Data to Mopy\Data.
Should be doable with an ini setting. Most of the directories are customizable now, so it'd just be an extension of what's done.
- Tweak Names for spells takes the spell school from the first spell effect rather than the most expensive spell effect as it should.
I've no opinion one way or the other, but it'd be easy to implement.
- Bash.ini field for the directory used for hidden installer archives.
Can be done. Should it? I don't know. With most of the other directories customizable now, I suppose it makes sense. But, it might have some unintended consequences.
- Right-click -> Move to Top/Bottom for plugins.
Use the Redate function. No sense in duplicating functionality.
- Right-click header -> Check/Uncheck all for plugins.
You can check/uncheck all selected mods by pressing the space bar. For now, you can select them all by clicking the first mod, scrolling to the last mod, hold shift and select the last mod. Then you can use the space bar to check/uncheck all of them.
It'd make sense to have ctrl+a select all mods (I'm surprised it doesn't already), and then you could press ctrl+a, then the space bar for the same functionality.
- Right-click -> Rename for installers.
Isn't that already supported? It's right below "Hide..." on the context menu.
- Right-click header -> Add Separator in the plugin and installer tabs, to place a ==Separator== for organization.
- Dummy separator plugins that start with == should be gray like ==Last== in installers
Agreed. This would need a bit more work than most of your ideas, but it's mostly implemented on the back-end. One potential issue is that there might be a few places that assume the ==Last== separator is unique, so some testing would be needed.
On the whole, as far as I'm concerned, they're pretty good suggestions. If the maintainers agree is another story

Until I get developer access to the Bash svn, I don't plan to make any substantive improvements to the Bash code. I'll fix bugs, but it isn't fair to Lojack to have to do all my commits for me (which I do appreciate, btw). I do have access to Bash's TESNexus page, but then any changes I made wouldn't be reflected in the svn and just make more work for the others.