It's nice hearing that people are liking my mod! Now I just need someone to do a Let's Play of it---hint hint.
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The scope of each mod is wide, so listing the attributes it changes is going to make them all look alike. I think the best way is to point out just what makes each one stand out on its own. Now I don't have much experience with most mods other than my own--at least in terms of gameplay--but from what I've seen picking through them and hearing others say about them, here's how I feel they stand apart:
Final Mod Pack: enormous mod compilation, adds all of the old popular mods together with minimum changes to make them fit and balance together. Difficulty: I think it's harder? I don't know.
Area 51: focuses on adding a richer story to the X-Com canon, with more aliens and much more variety in activity. It also has human factions and starts much earlier in the project's history. Difficulty: A lot harder than the original, but not hard by veteran player standards.
The X-Com Files: heavily inspired by Area 51, it merges the popular points of Final Mod Pack and Area 51 into a rich and diverse total conversion which greatly fleshes out the story and lore, all in a canon-friendly format. Difficulty: I think similar to Area 51.
Reaver's Faithful: It's supposed to maintain the feel of the game, though it packs in so many balance changes that it really is a new experience. The general rule is that you are always presented with a choice, and everything you discover is valuable to you. Difficulty: wider variance depending on difficulty selection.
Hardmode Expansion: This mod adds a lot of new vanilla-style content such as new UFOs and weapons/equipment. It is not only much more difficult, but it gives you the tools you need to succeed, and it is up to you to figure out how to use them. The mod has been popular with players who grew tired of cheesing their way through the easily-exploitable vanilla game. Difficulty: much harder than original, hard even to veteran players.
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I feel I should mention X-Pirates. It's not actually set in a different universe, but rather in a possible distant future, a post-apocalyptic world picking up its remains after losing a war with the aliens. It focuses on human-muton hybrid women who escape a scientific research facility to strike out on their own, and their struggle to build their home from the ground up despite being in a hostile world, scarce resources, and everyone distrusting mutants like them. The game has a very rich and intelligent lore, and is filled with self-awareness, genre-savvy, and meta humor. And lots of mutant porn. Difficulty: much harder than original.
Xeno-Operations also deserves a mention though I don't know anything about it's style. It has great graphics! Someone started a Xeno-Operations Let's Play recently so I suppose soon I will become more familiar with it.
Another mega-mod I don't hear mentioned much is Xtreme Measures. I played it briefly. What I noticed most immediately is that it offers lots of weapons and terrain, and it makes the tanks extremely powerful. I think it shares a variety of features from other mods. Difficulty: I didn't play enough to know, but it appears to be significantly easier than the original.
Everybody's favorite 1.0 megamod is AwesomeGuns. This mod is designed to be played on the ancient milestone. It not only adds lots of weapons and changes the existing weapons for an enhanced visual and sound experience, but it also changes a lot of the gameplay in other ways, as well as the enemies you fight. Some of the weapons are much stronger, but don't be fooled because you need them! Difficulty: significantly harder than the original.
From The Apocalypse is like X-Pirates in that it is highly different yet set in the same universe. In FTA's case, it is essentially X-Com Apocalypse in the style of UFO Defense, taking cues from Area-51 perhaps and showing how the various human organizations interact around the globe. Very interesting, very different from vanilla. Difficulty: in my limited playing, I felt it was similar to the original.
I think Tech-Comm might be the only megamod/total conversion I know of that's actually set in a different universe. (I don't know anything about it.)
I don't have any experience with UNEXCOM but I think I'll have to give it a look as it sounds pretty cool!