Well, I havent started on EQ2 yet, but Ive been playing MMORPGS since UO beta (which was just before EQ1 went live), and Ive recently expeienced the same feelings about FFXI as you.
When I look back at the game, there are a few things that they definately did wrong.
Travel - I like how they added Chocos to keep true to FFXI, but honestly, it made the game boring as hell. The travel times consumed a lot of playtime and Im sure this discouraged a lot of people. Now there were warps from WHMs and BLMs, but when one wasnt around, the game became tiresome. Airships were also in the game, but you werent able to access those until much later.
Partying - While the partying idea is fun, FFXI did it to death. If you didnt have a party in FFXI, there really werent a whole lot of things that you could do. On top of that, many people spent hours upon hours waiting for a party. Another thing that turns people off.
Repitition - So you play the game to level 18...Get a subjob...and...do it all again?! I must have done some things in that game 5/10/15 times over and it just becomes so boring. For example, almost every experienced player had been through the Valkrum Dunes 10 times. Thats more that any player should.
These were just a few of my main concerns about the game. I had a few more, but these are some that stick out in my mind.