Both post-99 systems are a mess in how they were implemented (Item Level & Job Points). There's nothing wrong with the idea of creating a way for players to progress and ascend, to stagnate too much would make players lose interest. I think most of community agrees on this.

Concerning specifically Job Points, I feel they could have done a better job in communicating their intent. While I realize no one (or company) is perfect, from a constructive criticism standpoint they could stand to be more clear with their future vision of level increases - even if it changes in a matter of months from being a casual edge to a new level progression system.

My personal concerns with Job Points are "fixing" jobs with them. I say fix in quotes because I'm not trying to say these jobs have zero use, but they do have flaws which have been brought up by the community. If there is an overarching issue with a job, it should be directly applied to the job itself. Some jobs have gotten that treatment directly in the past year to correct things (GEO, DRG, PUP, SMN, NIN, etc.) They didn't require additional grinding beyond being level 99. They were just remedied, and I would feel the exact same way if these were added merit points which are easier to accumulate.

Some commonly voiced issues I've seen is pet stats not being enough for content through accuracy, attack or survivability. Also Blue Mage, with additional effects of spells have poor accuracy and set point issues (especially now with the growing set number rate). However, unlike the other jobs it was applied to job points. Blue Mage in particular isn't some helpless job, but that doesn't affect the validity of expecting it to be directly applied to the job.

I can understand the concern of some players that they might be also trying to fix Elemental Magic falling behind with Job Points/Gifts given the announcement of these spells shortly after announcing they are making adjustments to Elemental Magic next. This is a case where it would be beneficial for SE to be a little more clear with communication and explain their plans for Elemental Magic, just as they did with the previous Elemental Magic update.

I'm all for 6 man parties again if that's their agenda for Job Points/Gifts. However, they need to balance jobs more so they are desirable to take to Job Points parties and you aren't stuck with the same bandwagon of jobs. While it might not be the case yet as you pretty much try to take whoever will do them right now. If they continue in the aspect of making it a true level expansion system, players will start to optimize and exclude when desirability rises, like any other content.

(geez... that was a long post. sorry)