After spending several days of pen-and-paper testing in the mountains (well, yeah, I did stay there for a month), I came up with two options to deal with the Fighters vs Mages MP usage and rune slots problem.
1. Tie maximum MP to character levels as well as MAG. This allows pure fighters who will only try to raise their MAG to increase their maximum MP to use their command rune skills more often to do so through equipment and not by stat allocation before or during the game. At the same time, it also allows caster-type Rune Knights like Flik and Geddoe to spam spells and dish out physical damage as well (though the latter part may require better thinking). Therefore, minimum MP at certain levels should be agreed on. One could ask, "Should a pure fighter ever have a level 4 MP slot when command runes take up only 3 MP level slots tops?"
2. Similar to Tactics, base everyone's MP to the SKL stat, except for Mages who will base their MP on their MAG stat. This system, however, would make caster-type Rune Knights and Rune Archers less effective than they are in say, the first three Suikodens (I don't count S4 unless anyone can name for me a decent-to-very-good RK in that game; S5's revamped Magic Sword system made all caster RK's but Shield Rune bearers absolutely useless, which I would explain later), as they will never obtain a fourth MP level slot unlike the Mages. The only way to obtain a fourth MP level slot would be making a Mage wield a long-range weapon, similar to Ted and Zerase.
The reasons why RK's and RA's are overpowered in Suikoden is that 1) they have more rune slots and skill slots than pure fighters, 2) they have the same access to level 4 spells that pure mages also have, and 3) they can normally attack unlike pure mages and can spam high-level spells unlike pure fighters (but at least the latter can spam their command runes all day long, so they still have an edge even over Magic Sword RK's).
The Magic Sword Runes, however, made caster-type RK's useless because why would you want to spam spells when you can just buff yourself with Magic Sword and deal damage at par with a fourth level spell from a higher-order elemental rune PER SINGLE STRIKE, or that of a pure fighter with a Fury Rune? If you want to be a caster-type RK, just wield supportive runes like Water, Earth, or Shield instead and leave the offensive spells to the pure mages.
As for the rune slots, maybe we should give the mages 3 slots, 2 slots for everyone else. Otherwise, I could see 3-slotted fighters overpowering pretty much everyone.
And as for spells we don't ever use like Wind of Sleep, how about making it 100% effective, the only things that will make it not work is the enemy's MDEF and Wind and Sleep resistances? Silent Lake can be used tactically, especially in PvP and Nation Wars. Have a whole army of Fury/Double-Strike fighters escort the Wind and Water Mages, then have them chase after the enemy spell casters. Once in range, the Wind Mage casts Wind of Sleep, the Water Mage Silent Lake, and then the Fury/DS will finish them off. As we all know, spellcasters are sitting ducks for Silent Lake.
Any comments or suggestions?
It's not all about knowledge, but it helps.