(Forewarning: Most of this is just my throwing thoughts out as they occur; don't take anything too seriously as a criticism or anything.)
Enemy Lancers have trouble getting Jump off, frequently have terrible Jump range, and generally suck anyway, is my feeling. (Granted, LFT may have changed this, but... IIRC in the older version we played we steamrolled the 3? battles that had Lancers badly, so eh, can't comment.) I'd put performance of the PC version higher. That said, yeah, earlygame lance (after Zeklaus at the latest) would solve my complaint here.
Enemy Samurais you don't worry about for their physical anyway (random Brave doesn't help them), and they are few enough you could lock their weapons without mega headaches if the idea of seeing one with an Air Knife bothers you. This strikes me as better than bringing Asura too early for reasons you already brought up.
Calculators with Staves (or whatever) seems like it has no drawback at all.
A Wizard with a Mithril Knife does 16 damage, which is bad but a hell of a lot better than 6 damage, which is what a female Wizard currently does. (Males do 9.) By the time elemental Rods show up, Blind Knife shows up and it's 20 damage. I don't agree that a 25% randocast is better than this at all, though of course the element strengthening is indeed far more important. If you're worried about some enemy Wizards losing strengthening (never mind all the ones with Rods/Poison Rods have nothing to lose), though, you can compensate for this by making more of them female or improve them in other ways. (JLevels, fixed Faith, fixed equipment, fixed support ability, etc.)
Granted, this doesn't matter for Wizards tooo much, since it's purely flavour. In general, though, my kneejerk would be that it makes more sense to balance things for the PC end first and worry about fallout on the enemy end as a secondary, especially for more rarely-used jobs because it's easier to do manual fixes if need be. Heck, you don't even have to fix every enemy - enemies were nowhere near optimised in original FFT (male 45 Faith Poison Rod/Headgear Wizard!) and a little thing like the odd sword Lancer (which, incidentally, is still better than a vanilla FFT enemy Knight) isn't going to bother anyone.