Merits as presented in FFXI were inherently flawed in design. Most of the "choices" weren't real choices at all. A DRK could opt to spend their points in stuff like Souleater recast, or could waste them in Weapon Bash recast.
It was worse for mages because they were funneled into specific categories. BLMs were funneled into either Thunder Potency (then taking Blast II) or Ice Potency (then taking Freeze II) since that's what got you the most bang for your buck (which was a big "fuck you" from the game to you if you liked earth, fire,water or wind as your chosen element). RDMs had a similar problem, though it was basically just Ice Accuracy merits. I personally felt the sting from that one since I like fire on my mages. It's not a system I'd want to emulate.
Fixed. You and I both know this sort of thing trickles down.
I'm more in favor of permanent choices rather than letting people change specs at will. Making it east to switch specs is part of why raiding turned into such a mess in WoW once they implemented dual specs. To XIV's benefit, we won't see raids telling people to spec for different roles (post-dual specs made being a paladin less fun, specially when all you wanted to do was smash faces with a light-imbued warhammer and they were asking you to get a healer or tank second spec), but it's still a pain.*While yes there is WoW and their tree I was actually thinking more Diablo 3, a lot went wrong but being able to make a build without seppuku was nice imo. They made you live with your build during combat but beyond that just switch out whatever wasn't working for your style or team.
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This said, I could go for something along the line of merit points gained from exp post-level cap, but only for RP-friendly or cosmetic stuff. Could be additional effects on certain abilities, different particle effects for certain spells (maybe have one where you can change the Stoneskin animations to be like they were in 1.0), or extra abilities exclusive to each job (say, give WHM the spell Float, but can only be used outside of combat and the effect fades as soon as you're attacked or you attack someone)