RUN is a perfect example. They specialize in Great Sword and can't access any REMs, can't unlock Empyrean WS, and have to use inferior options.
I know your say Relics were designed before BLU/COR/PUP/SCH/DNC/RUN/GEO came out and wouldn't be "balanced", but there's no real "balance" issue there at all. The game isn't going to implode upon itself into a singularity of failure if RUN gets put on Ragnarok, PUP on Spharai, or GEO on Claustrum.
RUN is held back by a lack or REM weapons, it can't get as much use out of Swords because almost all Sword WSes are garbage outside of Requiescat for special defense, and it can't unlock CDC.
Why do so many jobs have Archery and Marksmanship skill, but only one job gets native access to weapon skills for those weapons? No other weapons are like that, and I don't think opening all but a few WSes up to jobs meeting the skill requirements would be too damaging to anything. Samurais were pretty good at archery and SAM in game is on the relic bow, and are able to use Namas Arrow, but those mouth breathers can't even figure out how to use Flaming Arrow.
Can we get some more jobs on Arrows higher than ilvl 107?
More weapons other than a job's "main" weapon types would be nice, utility isn't a bad thing.
That's just a few examples of what I'm talking about. I like that the game is moving back towards more lateral progression, making more content relevant, and adding purpose to outdated events by using upgrades. I just have a problem with a few long standing issues that stand in the way of flexibility, utility, and common sense and are especially more poignant now that we're in an era of low man events, where said flexibility would be more beneficial than before.