TFTD's 50%-150% damage range instead of 0%-200% is HUGE. It makes armor massively more useful, and TFTD also has better (front) armor. Combined with the fact that alien weaponry doesn't have auto shot, it's literally impossible for a single alien to take down your end-game armored soldiers with sonic cannons. And when X-Com aliens would react with auto fire in horrible, horrible ways, TFTD's aliens can make max 1 snap shot. TFTD's starting tanks are nigh-invulnerable to the majority of alien starting weaponry.
Tentaculats appear way, way less often than Cryssalids did and never appear with civilians, so no instances of needing to fight 30 in a mission like you would if Cryssalids ate all the civvies. Flying was never really needed as a counter to Cryssalids, simply leveling the ground so they couldn't sneak up on you worked. Both are equally deadly in CQC missions inside the alien bases.
Cyberdisks, probably the #1 cause of early game mission failures in terror missions/base assaults, are gone (terror drones are cyberdisks 2.0 but are far later and rarer). In their place the terror troops for sectoids are arguably weaker than sectoids. The other ruiner of early games, alien PSI, is far weaker in TFTD aliends stat-wise, meaning far more soldiers can resist it well (instead its used slightly more often by weaker sectoid ranks, but in fact they are so weak that they can hardly affect anyone and it turns out to be good for psi-testing soldiers). It's also far weaker on the lizardmen compared to ethereals, and lizardmen are present in much smaller numbers since most of the end game is mixed aliens, so instead of 10+ psi attacks per round you'll have 5 or so.
Lobstermen, the one truly new and impressive alien, has a critical weakness to the Thermal Shock Launcher. And they really aren't that tough to sonic cannons either, they only really shine in CQC.
Far stronger alien grenades help players way more than aliens.
The TFTD's Triton is 100000000x better than the Skyranger. Skyranger is literally designed to kill soldiers from aliens shooting at their feet and costing tons of extra TU's to walk down the sloped surface. The Triton has a door. A motherfucking door, a marvel of modern engineering. I've cleaned half a terror map in TFTD just by peeking out with a tank, spotting something, throwing a grenade, then hiding behind the door again with everything before the alien turn. It's amazing glorious shit, to have 15+ aliens dead that have never had a chance to see you.
That said, the things that are legitimately harder in TFTD:
- Everything to do with multi-part missions, especially since they have lengthy CQC segments (fuck cruise ships especially). Arguably better to just abort the two part terror missions and wait till you have blaster bombs/psi for the bases.
- Larger levels in general require you to spread out more and be picked off easier.
- Far harder to level terrain in general (either through stronger objects or just plain hills instead of plains), compared to how easily barns blew up in X-Com.
- Rocket Launcher and Motion Tracker not being available above water hurts a lot. Blaster Bombs are arguably a toss up since the aliens can't use them either.
- Gauss being pretty gimped compared to lasers. But then Sonics were gimped far more for the aliens than you, and you can just rush Sonics.
- Alien sub and base layouts being very confusing and having way more blind corners to be shot at from.
- Strategically you can't cover most of the funding areas with just 3 bases like in X-Com (America/Euro/Asia).