I went more with defensive penalties over offence penalties because when you load up on Magic materia it can badly affect characters built for strength. Spells like Revive and buff/status magic are a good fit for strength-builds/tanks so they can take some of the MP/slots burden from the casters, but strength penalties make that less attractive. There's also hybrid builds that can use both, say spell + added cut, that benefit from not having strength penalties to deal with.
I personally found the Enemy Skill Materia to be the best option for Hybrids since it gave a ton of options for a mere single Materia Slot, and didn't ruin their defenses. Though I do see your point for them. As for Strength/Tank builds, I find the Status Effect Materia and Summon Materia work perfectly fine for Elemental Materia pairing and providing solid buffs to their important stats.
As for the slots, I knew that casters would want for them so I had the other type of gear have slightly better slots to make it less of an easy decision; the magic buff comes at a cost of less versatility in their slots in most cases. Strength-based characters can use their extra slots for utility Materia, like Sense or Barrier+All for instance.
early to mid game, there's not a whole lot of Materia that physical characters really want, so a Physical Aerith can easily do an Elemental=Status/Summon Materia, Added Effect=Status Materia, and Time/Barrier=All and have plenty of room to spare, while a Magical Cloud with the Mythril Saber and Silver Armlet has just enough for Recover=All, 3-4 Attack Spells, and 1-2 Command Materia depending on how many Magic Materia you give him.
Elemental and Added Effect offer a really good defensive buff if used properly against special attacks, so the defence loss helps account for it. I think it's the way to go with it, but I'm thinking of tweaking the elemental damage reduction itself in the final, which means I'll be adjusting the penalties on the Materia accordingly. I might make the Added Effect one different from the Elemental one.
At endgame, you're better off using Shield, so using Elemental defensively is kinda moot. Not to mention using Elemental defensively is fairly tricky outside of boss battles, since there's rarely, if any, locations where monsters primarily use one element.
Meanwhile Added Effect has strong usage both offensively and defensively with Contain and Hades being a thing. Though both of those are fairly late game, so Added Effect isn't very useful defensively until then. Lagomorph and Seal Materia keep it useful offensively, though.