New thoughts about magic system, maybe, as with the graphics and theme, it would make more sense to think about what resources I have available and change the game universe to match it. Gameplay first, not narrative first.
So I actually quite liked the magic/equipment system from my first RPGM-MV game, Grind Storm. Each character gets 1 weapon, 3 equipment and 3 "orbs". The orbs give you either a passive skill or a magic spell. They can also give more than one, for example, the Burn Orb could let you cast Burn and protect you from fire damage, the Freeze Orb could let you cast Freeze and add chance of freeze to your attacks, the Triple Threat Orb could let you Burn, Freeze or Shock, and so on. I would still want to incorporate the Orbs into the story. What are they made of? Where do they come from? It could be that, in this world, it's magic orbs instead of spices that are sparking the exploration of the New World and the East Indies. There might be no magic in "europe" or at least no orbs, and people are trading across the ocean to get them. Or, orbs could be a product of nature, so you might fire orbs in a volcano or in the desert, and ice orbs in the far north. This could be an interesting trading strategy thing for the player. Like if you're in the North, everything you fight is resistant to ice damage and freezing, but on your next voyage to down south the volcano, your ice orbs will give you a big advantage. (except I don't actually have a lot of biome graphics, so this is already breaking the rule of practicality) Or the orbs could be the remnants of a lost Atlantean culture, maybe not magic orbs per se but rayguns and gadgets. Atlantean relics could be rare in "europe" or they might have all been excavated already. So if magic is a finite resource, you're probably going to want to horde it rather than trade it, so trading spices and goods might be the main focus of trading mechanics and Atlantean relics are just for combat mechanics. Or the orbs could be gifts from the gods or eldritch things. If the eldritch things are indeed aliens, their gifts to their followers might be rayguns and gadgets.
I also like Final Fantasy Tactics' jobclass system, and Yanfly has a pretty extensive set of job class plugins to mimic FFT and similar games. In FFT, you can change jobclasses at will, outside of battle, so Fred could decide to be a Knight, Archer, Black Mage or White Mage. As you fight, you gain job points, which you can spend on abilities. So let's say that Fred decides to be a Black Mage for a while and earns 500JP. Fire/Ice/Thunder I each cost 250JP, while Fire/Ice/Thunder II each cost 500JP. So he could learn Fire I and Ice I or only Fire II. Once Fred has learned these spells as a Black Mage, he keeps them for other jobs, so he could switch to a Knight and still be able to cast his Black Mage spells. You would also unlock new jobclasses by gaining Job Points. So if you gain 1000JP at Black Mage, you unlock the Time Mage class, or if you gain 2000JP in Thief and 2000JP in Monk, you unlock the Ninja class. This is how Final Fantasy Tactics did it, I'm not 100% sure how much of that Yanfly was able to reproduce in RPG Maker, and I know that he added new things and he's taking inspiration from other series like Bravely Default, so I don't exactly what jobclass mechanics would be available to me. If part of the game is that you're able to recruit random characters in your travels, a randomized FFT style jobclass might be difficult, but Yanfly is usually pretty good at giving you control over his plugins.
Anyways, if I did a jobclass system, I might pick some classic D&D or Final Fantasy style classes, but I also have
that list of Modernesque jobclasses from before. I think I would not have some of the more futuristic or pop culture jobs like Cyborg or Super Spy or Magical Girl or Masked Hero, but a lot of them should work. Martialist, Buster Knight, Mad scientist (more of a steam-punk one), Ninja, Pirate, Gunslinger, Esper (possibly), Fencer, Reaper, Heavy, Warlord, Medic (possibly), Eldritch, should all work, I could also weave in a couple D&D/FF jobclasses to that, like a Rogue, Red Mage, Bard, but this is already more than I would actually want.
Another approach to jobclasses is to focus on real world piratey/age-of-sail jobs onboard a ship, such as Captain, Navigator, Accountant, Doctor, Carpenter/Shipwright/Boatswain, Gunner, Fighter, Cook, Entertainer, etc, and on a trading ship, you might have someone like Translators and Negociators. These would be not especially combat oriented, so combat abilities would come from equipment or race. Although these might be somehow combined with the other jobclass systems, so for example, you might assign your Warrior as Captain, your Black Mage as Navigator, your Thief as Shipwright, and your White Mage as Cook. I know that Yanfly has a plugin called Extra Character Variables, but I don't have a clue how I would achieve this. Also, this system of jobclasses doesn't suggest any visual difference, like how would a Navigator look different from the Boatswain? This might be a good thing, since it's less work.
Which does bring me to a point of thought, the characters I get to do myself, so I do get to and have to decide what to make them look like. I'm still doing the animal-people, so if there's jobclasses, there needs to be an array of each jobclass. However, I don't necessarily need to make a jobclass graphic like the ones in FFT, you'd be able to tell the difference between a Martialist and a Fencer and a Gun Slinger by how they are attacking. But I would also like to use versions of the playable characters as enemies, again like FFT does, and I definitely want there to be some visual distinction between the factions. In FFT, this is done with a simple palette swap, which would be simple enough to do with 3D graphics as well, although it might not be enough if you're trading with places like China and Japan and Indonesia, I might want them to have some kind of eastern version of the same jobclasses. I would actually love to have some kind of random clothing/appearance system like SimBro does. RPG Maker is kind of set up for that, but since I'm replacing its graphics with my graphics, and I want to make much more complicated animations, I don't know if that would still work.
On the subject of appearances, making clothing for 3D characters can be difficult, and I'm still exhausted from the holiday retail season, but there is a simple way out. Everybody is naked. This is actually a conclusion that I came to for my Bosstralia characters ages ago:
Spoiler (click to show/hide):
So they would look like this, naked, with the private parts washed out, and some kind of accessory that gives a sense of personality to them. This is not just about being lazy, but also when you're making animal people, you often want to have a character with spots or stripes or tufts or some specific coloration that lets you know what kind of animal it is, and clothing covers that up. But I think if I do the characters like this, any pornography would be pretty much impossible. It's still currently my plan to get something on Steam, so that doesn't really matter too much, but it's just a bridge that would have to be burned. And it wouldn't change my plans to use the same base models for pornographic artwork on the side.