On PC I believe there is a mod to allow you to manually equip everyone, I think it's just an .ini file change
It's one word. Change a word from False to True and you can fully equip them, but it does require some finessing to get the allies material requesting the new upgrade line.
But having read the wiki, I know the range of skills and classes and such now so I can't really be hyped for it any more. Urgh.
That's kinda your fault. Skill system is somewhat different from normal SaGa because it's not RNG, but deterministic based on skill levels you can't see.
Finally broke down and checked a wiki when I reached that god awful desert quest. After walking around for fucking ages to hit all those markers, some douche appears somewhere in the massive zone and I'm supposed to find him? Fuuuuuck that.
That whole zone blows, but once you get the map it's much easier.
And then characters have weird mystery stats like 'Gluttony' or 'Love' or 'Handiness'. Which affects the AI? Jesus christ.
As I understand it, the 4th stat's name is irrelevant but as it goes up the character becomes more of a "team player" and will reassess more often in battle if the conditions call for it. Amongst other things.
so there's no real consequences, and again, you've got little control over things.
Saving wherever has always been a SaGa thing, you shouldn't be this surprised. You have plenty of control over things if you disable amd enable all the skills you want them to use, and have the AP for it. Mixing physical and magical, however, is in most cases bad because they tend to conflict with the AI of certain classes. Top tier classes are intended to be extremely difficult only available to a few people because of how powerful they are, as well as being intended specifically for someone who's going to lead a Union.
You'll often get turns where your guys just don't want to fucking heal themselves or use any of their powerful moves.
Everyone ignores base / Max AP and wonders why they don't use their strong attacks. If you have 100 AP for the union, you're probably not going to get a turn that uses 90 of it. Also, Morale factors in the attacks used. Higher Morale means better Skill usage, but stronger enemies typically rule the Morale Bar.
As for the healing bit, i have no idea. I've played the game 4 times and unions not healing themselves has never been an issue. You need to know that certain Command types in battle allow for units to make assessments as necessary during the turn, while others lock them into place (i.e. "Attack with <type> Arts!" will never cause a wounded ally to change his basic attack to Revitalize, while "Give it everything you've got!" or whatever will cause allies to reassess on the fly and heal as necessary) action-wise.