I suppose Jem could have been live-action if Christy Marx (the de facto "creator" of the TV show; and yes I know that the IP was Hasbro's creation) wanted it that way. However, I personally think that animation was the right medium for this show. Otherwise, it would have just another generic drama series (aimed at the parents, even). Thus, if this show ever got remade, I would like to see it animated, because live-action would at this point be far too predictable.
The same principle above also applies to Maxie's World (based on another Hasbro property).
Devlin (one of H-B's very few dramatic series) could have been live-action, I guess. Then again there's the matter of the title character being a motorcycle daredevil...
Heck, I'll go ahead and say it: the 1973 version of Charlotte's Web could have been live-action, or at the very least live-action with animated animals (The Incredible Mr. Limpet, anyone?).
Strawberry Shortcake (both the 1980's and 2000's versions) can actually work in either medium. Yes, that's right: live-action complete with the franchise's same fantasyland setting we all know and love.
That's all I can think of at the moment.