Controls are better in God Eater 2 in general as there is no weird input lag caused by the animations, esp when it comes to turning around in a different direction and attempting to shoot at the same time. Which can cause some irritating as shit situations.
https://www.youtube.com/watch?v=EEv7BnvntD8
link provided is my vid of me playing at the start of the game (its just a demo showing off the ps vita tv) but gives you an idea of how the movement is. And you can see my character dodging and blocking attacks among the melee system which has been greatly improved over the first God Eater.
Everything is fairly straight forward in terms of controls too so its nothing overly complex. If you have played other titles in the genre before then you will have zero issues. Even less if you obviously played the first one.
You need to be more specific when you say customization. Generally GE2 its far easier to enjoy weapons that you create and understand all of the skill additions that equipment has. Not to mention its not randomized like Freedom Wars.
There is no "armor" in the game like freedom wars and clothing is just purely cosmetic. Freedom Wars the outfits are all a single piece, though there are multiple versions of the same one by pressing the square button. God Eater 2 its broken up into tops / bottoms. While freedom wars has some nice outfits, overall some are quite disappointing as they were obviously not made with care as hair clips through a lot of various models so things like hats that can change hairstyle mess with some outfits closing out potential combination possibilities. God Eater 2 is better with being careful with this personally. Its a damned shame too since the nice looking outfits in Freedom Wars are great. Coloring outfits more detail goes to Freedom Wars as its sections that you can change the colors of with the color sets available to you. The decal system while neat its personally shit due to the terrible locations that are all preset and you dont have freedom to move them around to any spot as you please. Then depending on the face type too it seems that some of the facial decals will not fit properly either even if you try to resize them.
In terms of numbers of weapons do think God Eater 2 has more than Freedom Wars. But thats expected considering God Eater 2 has weapons from the first God Eater also in it. Also with what weapons turn out to be useful God Eater 2 has better balance. But that once again is due to the game having 3 versions. God Eater, God Eater Burst and now God Eater 2. With freedom wars if you really want to kill things fast you will most likely be winding up using short range burst fire rifle. As it pretty much has the most efficient damage output when you go and latch yourself to an enemy. A guy I know his friend can kill the last boss in under a minute basically now with his setup. Saw the video on that.
End game content it depends on what you are looking for. Though Id have to imagine that GE2 has more content currently just due to the constant free DLC missions and such that they kept adding over a period of time. Freedom Wars will be just starting for that, so there is that to think of. Also for the time being Freedom Wars has less weapons in general, but thats just due to it being the first title in its "series" so to speak, so dont really hold that against it. One thing for sure with Freedom Wars is that you will be spending more time with trying to make a perfect weapon to do get the damage up to par for going against the stronger special abductors that appear in the tenbatsu missions. Since for those you need some serious damage which means you need to get all the best skills for the weapon (damage the most important) so kinda lost interest with that personally and hence why I had stopped playing, then again but have other titles to deal with also including OTs to make. God Eater 2 has some side story related paid DLC which was also released recently.
Overall content wise we can say for the time being that while its not as pretty map wise due to it having to "share" with the PSP gameplay wise Id say God Eater 2 has content down beat. Also the melee / ranged combat is far more balanced than in Freedom Wars where its mostly you shooting the shit out of stuff vs switching between melee and ranged. This is due to how the abductors are designed also and the way the game plays in general. So folks saying its more like a TPS that something part of the "hunting" genre are not wrong as you will be shooting a lot more than actually doing any sort of melee combos and such. As its generally just not efficient and a good way to get yourself killed.