While the fact that holy has nothing to do with the lily system in spite of its animation is disappointing, and its 10 potency increase despite going up 2 whole "levels" being fairly pathetic, I think its basically fine other than that mechanically. It does have a secondary effect too, it stun all targets hit for 4 second up like 8 or so second if spammed so I think holy is what it should be, except for the cast time, 100% agree it should be 1.5 sec, same for all healers main single target and aoe spells.

Thin Air dose need to be improved, though at this point I think my favorite idea for a change to thin air is simply for it to restore like 15% mana on use and be the same otherwise, 2 stacks 60 sec cd. While it would arguable be "weaker" than even its current iteration for rezing, I think its utility would over all sky rocket. This would also remove the weaving issue as you could cast it retroactively instead of proactively.

Aquaveil being 10 second would be cool, and another QoL change but I think its such a simple but effective ability to start that like you said its not a huge deal.

I disagree that making Afflatus dps neutral would make it too strong. Doing this would effectively give whm 1 extra glare every 1.5 min (a little more because Square didn't adjust Afflatus at the start like they should have) which really is not very much.

I hadn't thought about a second charge on Assize but that would be a massive QoL change, 100% agree. A second charge of Assize would make a big difference is how good whm feels to play.