EXP is still EXP even if you call it a "skill orb" or whatever. It's also EXP even if it's gained through incremental action—that means you, SaGa Series.

Chrono Cross does technically have levels, but they are so meaningless that I figured I'd include it anyway (since it's EXPless). Mana Khemia is an anomaly; it does have a leveling system, but it is presented in the form of a crafting system. Riviera is sort of similar in that your levels come from "mastering" items.