I must say, even though I think that overall the old X-coms were better, the new XCOM was still really good. It made the change from having a large squad of not-so capable fodder to having a small team of supersoldiers (at least in the end game). That said, some things were clearly lacking or flawed. Below is a list of things that will make the next XCOM a legendary successor and a great game:
1. Different ammo types. I fell in love with the Apocolypse auto cannon because it was a readily available, easy to use, and versatile tool that sported armor-piercing, high explosive, and incendiary rounds! I need my incendiary again damn it! You could sweep an entire battlefield and kill all the enemy without ever seeing them. They could be equipment easy to implement.
2. Wider arsenal. This is something the new game actually did fairly well. UFO: Enemy Unknwon only had pistols, rifles, and heavies. The new game added sniper rifles, and light rifles(plasma only, unfortunetly) in the case of weapons, which was okay. Where it shined was the armor selection. You had the first available carapace, decent armor, skeleton, a cheap, quick moving, almost as protective as carapace, with a grapple. Then you Titan which was all health and protection. Archangel: flight, good health. Ghost: Invisibility, grapple, 8 health, environmental protection (a little better than all others, Jack of all trades, master of all, but very expensive in money and elerium) and Psi-armor which is self explanatory. Expand the weapons and keep doing what you're doing armor-wise.
3. Free aiming! I want to shoot out cover and destroy the battlefield to make it a giant death zone for the enemies. If I have a feeling the enemy is there, why can't I shoot and find out.
4. Shots traveling. Alright, maybe I missed that muton, but the shot shouldn't pass right through his buddy I saw it clearly pass though.
5. Inventory management mid-mission. My soldiers should be able to pick up weapons or equipment from that dead or knocked out soldier.
6. If this is going to be apocolypse, please get the politics and relations system right this time. The original was basic, but you have the time and technology to do better.
7. Aliens need to stop teleporting, unless they have some sort of teleporting technology which would be cool and frightening if it existed, but does not officially exist.
8. Continue expanding psionics and make it a gameplay factor throughout. The new psionics abilities were really cool and versatile, and it was a shame they could only be used in the end game.