Exactly that, a mechanic whereby you build up mob abilities such as flying and underwater movement. Maybe as simple as kill more mobs to get a permanent or temporary bonus, or some way of spending XP to improve abilities. Maybe wearing a mob head could boost mob abilities. You know, just more stuff to do. More game to play.
I don't think it makes sense that way IMHO. For instance, bat's are flying creatures. If you can morph into a bat you shouldn't have to then earn the ability to fly. Flying is inherent to being a bat. Likewise breathing underwater is inherent to being a squid and for forth.
That's why I suggested the mechanic from my previous post. Player's should be made to search for the ability to morph by acquiring an item and or mob. The ability to morph should be similar to lycanthropy, in that its tied to the phases of the moon in terms of duration of the morph.
Imagine this. You have to search for this mysterious morphing creature that you can only distinguish by seeing it morph into another creature at a frequency of spawning and a rate of morphing that can be set by parameters editable by admins. Once you identify this creature is a "morpher" you need to capture it and keep it alive in captivity. Also you need to build a multi block structure of some sort to harness its ability to morph and pair it with an enchant on armor of a particular type that you wear in order to gain the morphing abilities. While you are morphed you have only the natural hearts and armor rating that the mob has. Maybe these ratings are improved by potions by some duration. In order to gain a new morph you now have to capture the mob and "give it" to the Morpher so it may learn to shift into that mob. There are several methods to capture the mobs currently available in vanilla and in other mods, but maybe a method unique to this mod could be added.
Once the forms of morphs are gained the abilities (e.g. flight for bats, fire resistance for blaze, etc…) are not restricted. What may be restricted is the duration and the frequency that morphing is available based on the phase of the moon. Full moon = full duration regardless of day or night. During new moon the duration is short and the frequency that you can morph is reduced.
Maybe you also need to keep the Morpher fed to sustain it's life. You could also "milk it" for a liquid ingredient essential for morphing potions…Maybe that ingredient is produced more during the full moon phase? Just brainstorming here. Open for comment or more ideas to keep the conversation going. The point being that I think there are more creative ways to balance the mod that lead to more engrossing game play.