I'm agreed that the game can't be a carbon copy of FFXI. FFXI was fairly successful in its time, but that was 8 years ago. The industry, and people's expectations, have changed. The majority of people playing FFXIV currently have a bias as many of us are longtime FFXI players (myself included), but we and SE have to accept that it's time to think outside the box, to use a cliche.

That said, there are some things I would like to see:
-Mog Houses. However, I'm aware that the time and effort it would take to implement these would probably be prohibitive, but maybe as a feature in an expansion. They were one of my favorite things in FFXI and helped distinguish it for me since player housing in MMOs is pretty rare.
-An AH. the FFXI AH wasn't perfect, but it was still much more efficient and intuitive than the wards system is, even with all the changes that have been made. In fact, I much preferred the AH/MH combo to the retainer system, but I know a changeover would take a lot of man-hours.
-Chocobos/Airships. I know this is well established already, but as an addendum I'd like a breeding minigame that doesn't take weeks and exactly timing logins. I think ideally, everyone should have their own chocobo to encourage attachment to the game, so the ffxi breeding system would be a poor system to go with this idea.
-Character search, as an addition to the useful but convoluted system currently in place, rather than completely replacing it. I also think people should be able to invite people to their party and linkshell no matter where they or the other person are. Both the FFXI and FFXIV systems for party invites are unnecessary hoop-jumping timesinks that don't add anything to the game except mild annoyance.
-Savng the equipment I had on when I changed jobs automatically. This, again, is to reduce the amount of time wasted in menus and increase the time actually doing things

I can't think of anything else offhand.