The problem is the group size. Since now in this game you need 1 tank and 1 healer for every 2DPS, the DPs will have to wait longer. The group should be 5 if not 6, 1 Healer, 1 Tank and 3-4 DPS.
I rolled a Tank because I knew this would be an issue. People just do not want to play tanks or healers in these games because those roles carry too much responsibility. So there is probably a 10:1 ratio of DPs to healers and tanks, and with a party of 4? This is why you will see long queue times.
Also I agree about the FATEs, they need to be nerfed or dungeons need to be buffed. If there is 4-5 methods of EXP gain in a game and everyone just chooses one method, chances are its not balanced correctly.
