I think a new set of missions that focuses on the modern state of things in Jeuno would be nice. Jeuno missions would be very interesting. I think it'd be cool if it were able to cross over and involve all 4 expansions in its progress, for once. Having new missions that require the completion of prior ones is something I'd welcome too. There are a whole lot of mission enthusiasts out there who would pounce on these, and its satisfying to know that our effort to follow the missions isn't unrewarded.

Ideally, I'd love to see the stories for unexplored continents, of course. My destination of choice would be the Mithran continent of Olzhirya, especially the Gha Naboh Matriarchate, and also including the islands of Tsahya and Zhwa. But any new area would be great. It's been a very long time since I felt like there was something truly new in FFXI anymore - new areas fueled my wanderlust. At times I felt that there may have been too many in the past.. and not enough anymore.
And technically speaking we did get 10 "new" areas through Abyssea last year.. except that none of them were really new.

Gameplay-wise, I really love missions because it introduces amazing battlefields to the game that don't necessarily involve drops and so on. This was my favorite aspect to battles like "The Celestial Nexus" vs Eald'narche and "One to be Feared" vs Ultima/Omega.
As far as the newest missions were concerned, I felt that they could have made them a little more challenging, since EXP loss has been removed, in effect making the missions feel more rewarding upon completion (in some ways like CoP difficulty), but without EXP penalty or the need to do preparation quest or have some kind of limitation imposed on the number of times you can try the fight.

If other aspects of the game are being raised to meet the future 99 cap, I expect for more content in terms of missions to come along too, and also to provide such a challenge for players. That's what I feel anyway. But there's been no news of additional mission content at all, so we can only wait.

Anyway, FFXI's 10th anniversary is coming up in like 7 months time.. Maybe the devs will have plans for something special then? Here's hoping.