Actually, Wizardry didn't do that. Wizardry 6-8 did adopt such a mechanic, however, though the specific example you cited is only true in Wizardry 8.

I could partially add Quest 64 to the list. Your elements level through conventional XP and through finding spirits (and there's no reason to delay picking up spirits), but other stats level through use (aside from HP (and in the Japanese version, MP) gains from killing bosses).

The Nintendo DS remake of SaGa 3 also has stats increasing by usage, even during battle. (That game, unlike the SaGa 2 remake, had its game mechanics changed completely.)

Personally, I would prefer it if RPG developers got more creative with growth systems instead of using Level/XP systems in every RPG.

Incidentally, the game I am thinking of writing will use a growth system of this sort, though I have decided to include a mechanic I am currently calling "Stored XP" to allow an altenative way to boost less frequently used stats and skills.

I mentioned the SaGa 3 DS remake. SaGa 2 does this (for humans and Espers (mutants)), but the growth is too slow for my taste. (My fastest playthrough of the SaGa 2 remake was with 2 robots and 2 monsters.)

SaGa 1 does not do this. Humans gain stats solely by using buyable consumable items, and monsters transform with meat. Espers gain stats and skills after battle, but it is determined solely by the game's RNG rather than by your actions. (The RNG in this game is so appallingly bad (to the point of making casual play less fun) that I hesitate to call it "random"; in fact, when soloing SaGa 1, I have actually used luck manipulation to get past Ashura.)

Edit: Some other games I thought of:

Hybrid Heaven (Nintendo 64) does this: Use a specific body part a lot and it gets stronger. I believe there are even visual changes. (My favorite attack in that game is the head butt attack.)

The Quest for Glory series also does this. This case is interesting because there are a lot of non-combat skills such as climbing.

Btw I completely forgot about Dungeon Siege 1, 2. It had skill-based progression. It was done quite well, there were just 4 main skills to choose from. But those skills regulated stat growth, and Dungeon Siege II had talent trees' system on top of that.

That's why I only listed Wizardry 8 in my list. :-)