You DON'T use Prime version of a Warframe and rank them differently from their regular version. Quote, "Though its Prime version has more Health, Armor, and Energy Capacity, it is more or less the same as its normal version." THIS QUOTE EXACTLY APPLIES TO ALL PRIME VARIANTS, but adds nothing game changing or game breaking! If minor stats increase is what puts the normal variant in the lower tier, then this logic is extremely flawed, when there is not a game-changing or game-breaking difference between the normal and Prime variant. Whenever you can do with the Prime variant you can already achieve with the normal variant.
The only frame that is different in behavior is Excalibur Umbra, which may warrant it's own tier, depending on whom you ask.