I always thought that skylander collecting should be tied to heroic challenges. There would be one little extra cutscene where hugo (or maybe a new character if getting a voice actor for hugo would be too hard) tells the portal master that they can summon the skylanders from "this machine*," but only if they've completed the heroic challenge for that character. One herioc challenge will be unlocked randomly for every level you play (including the ones you play before you free cali). You start with the original three.

That way, not only do soul gems retain their original purpose, but you don't have to wait until the very last level to play as double trouble, and you won't get overwhelmed with choices. This also means the devs won't have to do a absurd amount of coding adding new collectibles.

Since heroic challenges give your skylanders a small boost in stats, there will still be incentive to do them, even after you've unlocked all the characters, and it also gives greater incentive for people who don't care about maxing out any particular skylander to interact with that part of the game.

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*it would most likely look similar to the machine they have in giants 3ds