The thing I like with Limitation (caveat: In theory! I haven't actually used it in play.) is that it scales.
Take The Catch: For a fairy-type character, you can actually go from Inhuman Toughness to Supernatural Toughness for free by RAW. There is no incentive to not make sure you have at least -4 worth of catch-affected powers, since Cold Iron is valued at +3. At the same time - any upgrades from that point pays full price.
Or Human Form: Billy has -6 worth of powers under Human Form - Claws, Pack Instincts, Strength and Speed. If you can find a motivation to have access to any of those outside wolf form, say Pack Instincts (worked so much with the Alphas) and Strength (minor part-body shapeshifting to increase power), this wouldn't actually cost any more despite having full-time access to half of what was previously only available in wolf form!
However - I see it as an either/or. You either go scaling Limitation or the much more math-light RAW with fixed rebates. I doubt I'd allow mixing!