Not a bad list, I'm assuming you're also going to be switching to a regular MP system instead of Spell Charges, since most modern FF fans don't seem to care for the old D&D system.
Actually, I'm glad you brought this up. I'm a fan of the spell charges, myself, and in all honesty I'm not sure what to do with them. I think it works fine in the famicom and DS version, but if one would overhaul III like I suggested here, you run into some problems. The main problem are mostly the new abilities of non-mage classes.

The spell charges always worked with 8 levels. You had 8 levels of charges, and the higher you went up the ladder, the less charges you had. But looking at the new list, not all jobs have enough abilities to add a move to every level of charges. Take my new Thief. WIth Thievery able to do 9999 damage, naturally you'd add a price for the power. Thus it gets a spell charge. But what of the rest of the Thief's abilities? Steal? Mug? Escape? Those never required MP costs in the past. What remains? Lucky Seven, Quick Hit, Thievery. What level of spell charge will they get? It seems logical they won't get three following levels (3, 4, 5, for example). So you'll have to spread them out, over a 3 x 8 spell roster. It'll look awful, to say the least, and very empty. If you have one big MP pool, this problem wouldn't rear its head. It's also very much the question if you could actually divide a Thief's abilities into 'levels' with Spell charges.

So it's an interesting problem here. I am a fan of Spell Charges, but I also understand that once you bring more abilities than just magic into your game, you'll have a problem on your hands. You hardly can have both MP for non-magic classes and Spell Charges for mages. So it either needs to be one or the other, and one big MP pool seems to be the way to go. On the other hand, it takes away the managing-factor of mages that I liked in III, in that you had to dose your spell usage and mages couldn't just spam Holy, Flare or Bahamut. Others will call that a hindrance, saying it limits the usefulness of offensive mages. So in the end, it comes down to a debate of old vs. new.

I think one thing I may add to Devout and Magus which would actually make them better than their previous counterparts and actually make them useful against, say a Sage, is that they gain MP saving bonuses with certain job levels up. Like at Level 3, their MP consumption is reduced by 10% and it can level up to maybe costing 1/2 the MP cost by end game.
It's definately worth looking into. This is one of the problem's you get by getting 'levelled up' jobs like White Mage ==> Devout ==> Sage. Though I seem to remember that in the DS remake, Sages had a smaller amount of MP charges for the higher spells than either Magus or Devout, so for a healer you were still better off with a Devout. (Preferably backed up by a Sage with the most vital White Magic, and the rest filled up with Black. So the Magus did kind of get left in the cold.) I'm not sure, I'd have to check my guide again, but I though Devout and Magus, aside from higher Spell Charges, also benefitted from higher stats for their respective magic than the Sage, but I'd have to check.

Bonusses or job benefits to make either of the specialists preferable over the do-it-all Sage are definately a good idea, though!

For the Sage, I'd return their ability to use Summons again and give them a minor Turbo MP effect with some of their level ups, like 10% more MP cost to raise Magic damage by 1.5x damage, and move it up so while the cost is higher than average, ultimately capping at 3x damage at 70% MP cost. Then all you have to do is either give Sage boosted MP for his stat growth, or you can implement an equipment system like Tactics or FFXII that can artificially increase MP and HP on the party just by having it equipped.
To be fair, I feel that the Turbo MP effect suggested here would actually be more beneficial for the Devout and Magus, to make them better choices for pure Black or White than the do-it-all Sage, while the Sage, with his lower MP pool, gets the reduced MP cost.

I'm also not sure about returning the Summoner-effect summons to sages. I always felt that it made Summoners obsolete, even more so than Magus or Devout. The DS remake, I felt, did it right by saying "You want summons? Take a summoner!", instead of allowing the Sage to do it too, like in the NES version. In the DS, I used the Sage more as a kind of support Mage, supporting my Devout with white magic when needed (especially in the final dungeon), casting Black when he could. It's also an opportunity for Black Magic to actually get used again (since, let's be honest, Summons kinda outshine BM. Flare is nice and all, but it ain't no Megaflare), because the Sage can't give you high Summons. This means Summons are still highly specialized magic only 1 job can fully use to its highest potential, and adding one to the party or not will be a more tactical decision. (Since you mostly have 2 physical classes and 2 magical ones, you'd have to pick: back-up healer, or damage dealer? Considering the brutal final areas, not a decision to be made lightly.)

I think the D&D system would be amazing if it was just tweaked a little. The problem is that the lower level spells are very weak end game, and you still don't get to use that many of them. IMO you should get like 99 charges of your rank 1-3 spells by the end of the game. They are doing less damage than your super charged physical attack characters, but at least the mage isn't standing around doing nothing until a tough enemy appears.
I like Spell Charges too, and they definately should be tweaked if they want to be kept by the overhaul. You also adress a very good point. Because of the low amount of spell charges (you only get like 8 lv 8 spell charges as a Devout or Magus, and only 4 as a Sage), you save them up for bosses, meaning most of the time your mages are sitting ducks for the rest of the game. This greatly lowers the use of Mages in FF III, which is a shame and should definately be adressed. In fact, I feel most of the series suffers from this phenomena, even those games without Spell Charges.

I do seem to remember having 99 lv 1 spells once I was lv 99, but again, what use does that have, like you said? Those spells are indeed incredibly weak, and I only ended up using them for curing on the overworld, to save my higher cure spells. And for Black Mages, this is even more dramatic, for what use are 99 fire spells in the endgame?

Doing away with the Spell Charges and having an MP pool would do away with this problem right away. So just like with Wolf's post, it comes down to a debate of old vs new: to keep the Spell Charges (and update them) or to do away with them?