From a quick run through magical beasts A to B in the MM, breath and gaze weapons look like a problem. You're giving the creature (or, more to the point, a player) the equivalent of anything from a 2nd to 6th level spell ability, only better, because supernatural abilities have many less options to counter them. How do you measure that - maybe against the sorceror levels needed to cast it at will? As warlock level equivalents? Does the Level Adjustment drop away at higher levels when a caster of equivalent level could also produce the same effect?
The ankheg's burrowing ability and tremorsense are interesting at most for a monster but should translate to a big Level Adjustment. They'd be incredibly useful to a PC.
Aranea: already a shapechanger - the template should include a clause to exclude such.
Blink dog: see breath weapons.
Behir, bulette: too large to qualify, unless the base creature is a giant, which has possibilities.
The ankheg's burrowing ability and tremorsense are interesting at most for a monster but should translate to a big Level Adjustment. They'd be incredibly useful to a PC.
Aranea: already a shapechanger - the template should include a clause to exclude such.
Blink dog: see breath weapons.
Behir, bulette: too large to qualify, unless the base creature is a giant, which has possibilities.