Aside from changing policy on third party tools to work with the community where possible and crack down on rule breaking where it isn't like other big MMO producers do, merits would probably be the next big thing to see changes.
Job specific and weapon skill categories would be uncapped, as would Combat Skills, Magic Skills, and the Other Category.
Enmity would be removed from the Other Category, and moved into its own category. This category would still have a cap of 5, as would HP/MP, and Attributes, which would retain current caps. Players would be able to change them between universal and job specific however, with all players starting out with a universal default, and changing to job specific would clone the default for all jobs, and reverting would lose all merits except for one job chosen.
Future merit categories would be guaranteed to be uncapped as a promise to players, however getting more merits past a certain amount would cost exponentially more experience points. Thus, you'd have the illusion of caps, but you could grind past them with more and more work. Alternatively it could cost Conquest Points, Allied Notes, or Imperial Standing depending on where you'd want to add incentive experience point gathering to unlock new categories, if you really want players to grind.
The first major new merit category would be "Racial Merits" which would be race specific. Their sole purpose would be to make difference races homogeneously powerful, so for example, a Galka's merits would be mostly unlocking more MP and CHR and a bit of stats here or there that a Galka is missing, whereas say a Hume would just be boosting a bit of every stat across the board. The merit options in this category would probably be named after the races or something relevant, and be tied to the races, so Hume merits for CHR, Galka merits for VIT/HP, Elvaan merits for STR/MND, Mithra merits for DEX/AGI, Tarutaru merits for INT/MP.
These would be tied to beating an expansion, probably Chains of Promanthia since it would make sense, and would take a small quest to unlock. This would gate out most players into having races still be important enough for any reasonable sticklers, but anyone arguing that breaking the in-game reason for different races having setbacks after a long drawn out ordeal and lots of work probably didn't want to be reasonable in the first place and thus can be ignored. This would strengthen players out so SE could delay other forms of power inflation with this as a time sink, and balance races so SE doesn't have to design around it, while having lazy players and dual box characters eat it on stat differences.
Future merit categories could then be much easier to design, since you could not have to worry about balancing something like "Haste Samba" with "Step Accuracy", but instead having obvious choices that everyone will grab first, then bonus choices that players can get if they're very dedicated to the job. If that wasn't enough grind, SE could also make Job Specific, Group III/IV be individually unlocked after doing some job specific quest to further cater to "special flowers" and "career X" players without totally screwing over anyone who just wants versatility, no matter how much work it takes.
Of course, this would all be done after LISTENING to player feedback, although I'm partial to ignoring people who want the game to permanently penalize players for making past choices. It is one thing to punish players temporarily for a decision, that happens, but non-banning punishments should never be permanent in a game that is played continuously, it is just bad design.