As the one who (I think) originally discovered this trick, I will just say PLEASE keep crate-jumping. For so many reasons. For one it brings back feel-good memories of bomb jumping in Super Metroid. For two, certain areas in the game (one of the ice age areas, I think, generates a huge number of tall cliffs with no backwall) are just no fun to traverse without this mechanic.
For three, it makes for awesome skill contests - one of the more fun things I've done in AVWW is challenge myself to beat blue amoeba without touching the ground by constantly switching between crate jumping and attacking.
I think it works well as one of those undocumented "secret features", much like bomb jumping or energy restore from Super Metroid.