I've always left Hugo as a plain old attacker. He does way too much damage to ever consider using any of the True Runes on him given his low magic affinity and lack of mage skills. That makes the True Fire rune perfect for him since anyone without a high rank Precision should never use fire and you can't give it to anyone that has that skill.
Geddoe makes an amazing lightning mage so I always leave the True Lightning rune on him.
Chris is in the same boat as Hugo but less useful imo because of her lower damage output and low magic therefore I always give her the True Water rune and let her take a bit of a back seat. The level 99 trick makes her a lot more powerful though if you use it.
As for other True rune users you really only have Sasarai and I do always use him.
Rody is my next go to mage.
Melville can hit very hard and Alanis makes a pretty decent mage and they do have a decent combo as well if you don't mind taking up two slots with them both.
Juan can be an absolute beast and between he and Hugo the rest of my party never even gets to draw their weapons.
as for runes I like going with Gale on my fighters if I have the space for it and Killer runes are also pretty good imo. It makes the Continual Attack + Heavy Damage combo hit even harder.
With the mages I usually try to specialize them in one magic type as much as I can and boost those abilities.
I usually don't have anyone who is specifically focused on being a healer but wherever I have slots I'll toss in some water or shield runes so that I have a few people who can do a bit of healing if necessary. That means i don't have to worry about losing my healer unless I lose half my party and if I lose half my party I'm probably in a fight I shouldn't be in.