In addition to Stop Wasting My Time (made by a very mysterious and handsome author) already mentioned, there are a few other time-saving mods I highly recommend:
- Instant Avenger Menu: Instantly move between rooms in the Avenger. Also speeds up Avatar Project updates.
- Evac all: Adds a button to evac all units at once, rather than having to do it one-by-one
- Overwatch all: Same, but for Overwatch.
- Strip Primary Weapons: Adds a button to remove all weapons from all non-mission soldiers before a mission.
- If you like to color-code your soldiers by class, Automatically Color Units or Character Pool Uniforms will save you time.
- No Startup Movies: Skips the movies at the start of the game, speeding up the initial load time.
- Always Show Shot BreakdownsAlways Show Shot Breakdowns: Saves you from having to click the left-arrow on the attack screen all the time (which is actually a bug)
Also, the "experimental mod" mentioned by the other answer, Ignore Missing Content Warning, allows you to force-load a save game created with mods that are no longer installed. You wouldn't want to do this with any mods that add actual content (new flags/models/weapons/classes etc.), but all of the mods listed here should be togglable at will.