Ok, here goes:
hmsongDispel Magic ---
When a spell lands on a target, if the target has Wall, code specifically checks if a spell is number (zero-based) 0x20, 0x23 or 0x26, to decide if it should bypass wall. This happens in code at addresses $D04CB6 (CMP #20), $D04CBA (CMP #23) and $D04CBE (CMP #26). I could probably rewrite code so that it checks for some flag on the incoming spell to decide if it bypasses Wall, but that's a fair bit of work so I'd need a reason to do it; your example of buffs bypassing Wall I don't consider adequate (Wall intentionally reflects buffs, so changing it just because of one dumb boss would mean changing tons of other circumstances when instead the boss could be changed to be less dumb).
Mana Beast ---
Here's Mana Beast AI spell assortment:
That doesn't cover the logic for how it decides what to cast. As you can see it "knows" more spells than it actually uses, and changing some of these would probably not interact well with its AI logic (e.g. it checks itself to see if it has Wall before casting Wall, but if you changed that spell, it wouldn't get the Wall buff, so would keep casting whatever spell replaces it since that spell wouldn't give it Wall).
Changing $C293D6 from BNE $93EE (RAW D0 16) to BNE $93DD (RAW D0 05) might make him start casting the other 4 self buffs, but they'd bounce off Wall. Changing $C293D0 into a jump (BRA $93DD, RAW 80 0B) to skip all the Wall logic, so he never Walls himself and just runs the other self buff logic might be somewhat functional. His AI logic (which appears to just be hardcoded and not using the boss AI scripting like the other bosses) in general would likely need some serious attention for him to suck less though.
Engulf (and Poison) ---
Next update will have Engulf damage scaled back from 1/32 of current health, to 1/64 of current health, so its damage is weaker than poison, but obviously it still paralyzes. When play testing, I found Engulf to be a bit too much, especially since I was adding it to new stuff willy-nilly. I'll probably be slapping it on the Rising Sun boomerang as well (I've been meaning to add a feature to stick some sort of effect on the 4 non-level-one weapons that don't have any effects).
20 Spell Slots ---
Not sure how possible it will be to give any of the additional spells to the player. Most spell stuff is very hardcoded. They're in groups of 6, per element, with each group divided in half for black and white (sprite / girl; intelligence / wisdom). I haven't verified, but I also suspect which elemental summon animation to show is hardcoded to be based on which of these spell groups the spell is in. Shade and Lumina also share one group with some special-case logic so the girl's spells in that group act as Lumina spells instead of Shade.
Spell Interruption ---
Pretty sure I'd said before I like this idea. Not sure yet how to make it work, but it's on my list of stuff to figure out. Overriding animations can be pretty difficult, on top of having to figure out the right way to handle checking spell casting state when taking damage to decide if interruption should happen.
Petrify ---
Yeah, petrify is a problem. I've always just had a personal rule to never use Stone Saber because it's boring (too good), but I should probably make something so that instead it's just a valid option and not stupid. Likely the first step will be to make it do 25% damage instead of 50%. Making petrified enemies immune to melee would just make it a damaging copy of frosty, making them immune to spells seems like an okay idea but I don't know that it would actually affect any gameplay decisions... maybe I can just make it increase the victim's physical defense while its on.
Status Effects ---
I'm pretty sure the reason there is so much overlap in the status effects is due to enemy status immunities. They wanted you to be able to paralyze enemy X and Y, but didn't want you to be able to simply use the same multi-targeted spell on every enemy. They gave the various forms of paralysis slight variation for flavor, but ultimately it looks like they primarily intended for them to be paralyzing. Frosty prevents physical damage due to animation issues. I suspect enemies being immune to moogle (which is fundamentally a paralysis) is also due to animation issues (enemy moogle form is like frosty form where it has a very small animation table).
Sword Orb Teleporter ---
Yes, the exit is intended to send you back to the entrance of the second floor. There's a limited number of doors in the game's data (1024 I think?); by sheer luck there was an unused one in Mana Fortress doors (a door from the Dark Lich's room back to the empty Mech Rider III fight room) that I repurposed to send you into the new area, but using up a second door for the exit would've been wasteful. Sending you back to the entrance also provides a penalty for killing the orb droppers too quickly without letting them split / self-replicate.
Harder Final Boss ---
I've been meaning to get that imported (all of Kethinov's hacks actually; it just takes time and I prioritize the ones I personally have interest in using).
Trim Portraits ---
The interface at the bottom of the screen during combat, player faces, player health, recharge %, charge bar, etc. is the HUD (heads-up display). In video game jargon, the HUD is the interface during normal gameplay that is overlaid on the gameplay view. The term comes from aircraft where information is projected onto the cockpit window so the pilot gets information without having to look away from the window (their head stays up, looking out the window, rather than down, looking at gauges, etc.).
The little face picture on the HUD is what this feature affects. Without any status effect, the sprite's hair extends to the corners of the frame their face is in; this fixes that so the corners are rounded like for the boy and girl. It also fixes some status effect pictures that poke out at some of the corners, like moogle and frosty.
MSU-1 ---
Great! Which file naming and organization did you end up using? Did you use the BAT file?
Pretty sure you're the first person to give me any feedback on that. I did the ZSNES MSU-1 stuff for my own benefit (I develop ROM hack stuff using Snes9x Debugger, Mesen-S and BSNES, but play for fun using ZSNES, and wanted to give the remake's music a fair shake, which I think is genuinely decent), so am personally happy with it, but if anyone else found issues with it I'd still want to fix them. Jamming MSU-1 capability into ZSNES was, uhm, fairly tricky, so there are some limitations that likely aren't worth improving, but I'm always interested in feedback (even if I can't or won't act on it).
Mr XElemental Weakness ---
Werewolf, Evil Sword, Mimic Box, and Marmablue should all be Luna element enemies, so with Balance\Luna_And_Dryad_Weaknesses On, they should be weak to Dryad.
Buzz Bee, Mushboom, Lullabud, PolterChair, Crawler, Pumpkin Bomb, Chess Knight, Mushgloom, Trap Flower, Metal Crawler, and Nitro Pumpkin should all be Dryad element enemies.
Shade / Lumina ---
While in character stats, the girl doesn't use the Shade slot and the Sprite doesn't use the Lumina slot, in spell data and related spell code, Shade and Lumina are merged into one element. The developers clearly set them up to function as a single elemental that happens to have more art and two diametrically opposed resist values.
Spell Slots ---
If I can sanely use any of the extra spell slots for characters I will, but it doesn't look terribly likely. There are lots of issues preventing it.
Dispel Magic ---
By "magic recoil" you mean the Magic_Recharging delay? That's a great idea.
Saber Buffs ---
I think you're overthinking the ease with which a saber buff can be cleared. It doesn't really matter that you can "cure" a saber buff by changing weapons; the important part of a boss casting a saber on you is that it makes you have to react in any way, even if that reaction is to simply switch weapons. The wrong way is like Trials of Mana where you get super boned if you have a party without saber spells available to overwrite one a boss casts on you; instead of being able to react to the boss's action, you basically can't do anything aside from dying to clear the buff, which is arguably a pretty unacceptable way to be expected to react.
That's my opinion though. What isn't my opinion is why it works the way it does: the end of a saber spell animation blindly overwrites the target's weapon palette but there's no code to save these new color values for reuse, so when you switch weapon, it loads up the new weapon's colors but there's no longer any info on the saber spell's colors (so to avoid an uncolored-by-saber-buff weapon, the developers set it to clear the buff on weapon change). It could be possible to save these colors and not have the buff stripped on weapon change. It would be incredibly impractical to save saber buff status per weapon. I'm not really interested in implementing either though; the way it works already is functional enough for my tastes.
(Evil) Shadow Saber ---
In my brief play-testing so far, I've found use for it by keeping it on the girl. I generally play as the girl, so directly control who she hits to avoid hitting ghost/undead enemies. I never use Evil Gate, even in its More Useful form, so didn't consider it a loss. I do conceptually like the synergy you propose would exist between More Useful Evil Gate and Shadow Saber, but again, a 4th spell for players is a tall order.
zoolgremlinShade / Lumina ---
I'm 99% sure the sprite and girl only getting one was an intentional design decision. It required a fair bit of code to have the two merged to be basically one elemental for the sake of data layout. Of all the requests for extended spell data, splitting these two elementals apart so the Sprite and Girl can each get three more spells, is probably the most possible, but don't hold your breath. Would have to track down all of the hardcoded stuff related to these two to get them untangled enough to shift the Lumina data down 6 spell slots, decouple the elemental names from the spell names (the elemental names use up the 8 spell name slots after Lucid Barrier), get the spell menu ring allowing both simultaneously, the magic stats screen (I expended the spell name list but not the spell description list), yeesh, just thinking about everything it would take is making me make a face like: -_-