Nothing is more natural than to compare FFXIV to FFXI. I expected things that worked in FFXI to be carried over into FFXIV, and if not, then I certainly hoped the innovations would be for the better.

Seek/Search

FFXI had group formation tools that worked, but could have been better. A party recruitment feature is a nice innovation compared to FFXI, but it fails on its own. Better to seek endlessly in FFXI than to use the FFXIV tool and wonder "is this thing on?" It boggles my mind that an MMO is released without a useful means of getting in parties. A year later and my mind is still BOGGLED!

Still, I didn't expect a system identical to FFXI, I expected something better. Seek and recruit on any/multiple jobs for different types of content. An auto-grouper like the proposed Content Finder would be a welcome tool in addition to more interactive group formation tools.

Guild Leves (Battle)

A variation on the leveling mechanic compared to FFXI. I like leves for solo/duo play, but they are a disappointment for party play. Groups of monsters instead of always a solo monster and the lack of fighting over monsters in popular camps are good innovations. But it seems to me that an MMO should be focused foremost on party play and I miss the party focused leveling of FFXI.

Battle Regimes

Compare to skillchains from FFXI. A greater variety of actions building toward a greater variety of effects. I like the innovation but the requirement of entering a Battle Regime Mode took away from the flow of combat. High marks for an attempt to promote teamwork though. I would say a good innovation over FFXI in principle, but needs better implementation.

Market Wards

Quaint, but inconvenient. Convenience wins when it comes to buying/selling goods. We want Amazon.com and they gave us a strip mall anchored by Bob's Misc. Mob Drops and Amy's Weaver Emporium. I'm not sure what I would prefer over the FFXI AH.

Crafting

I prefer FFXIV crafting over FFXI. Local leves allow leveling progress without the need to create and dump a bunch of useless leveling fodder. And the crafting mini-game is more interactive than the all-or-nothing FFXI method. But the mini-game really needs Quality to mean something. It should mean something for crafting leves and it should mean something for actual crafted products.

Indirectly crafting hurt FFXIV if it influenced the creation of the Market Wards as a place for crafters to showcase their goods. It also hurt the game if it dictated the lack of challenging mission battles in order to accommodate dedicated crafters.

Plenty of other features to consider, like NM spawn conditions, loot distribution mechanisms, auto-attack, LS tools, seamless zones, etc.., but all of it will be compared to FFXI and if it doesn't compare favorably, it will be harped on. Rightly so.