Supports Mix-ins - binary patches you can apply to vanilla files for script edits and property changes (such as hack all the things or making enemies chase pets).
Supports installing Custom DLC modules, like the controller support mod.
Can keep a database of basegame files so you can restore to a non-vanilla set of files.
Automatically backs up DLC and files for you when installing mods so you can restore in 2 clicks!.
Installing mods via injecting them automatically via ME3Explorer (or direct copy on the basegame files).
Mod Manager It's about 3 years old now, and supports a lot of things: Contrary to the title of my program it supports far more than Coalesced mods (v1 only supported coalesced, as we didn't have DLC editing back then). If you haven't seen ModMaker, you should really try it out, it saves tons of time, and you can fork other peoples mods. It works with my online Coalesced editor, ME3Tweaks ModMaker. I've got a couple thousand active users based on some telemetry on my site. I have just released Version 4 Beta 1 of my Mod Manager tool that acts as a mod installer/uninstaller for files in Mass Effect 3.