Levitate IS the reason it didn't get Tinted Lens. With the exception of Bronzong, NO Pokemon with Levitate has gotten another ability.
Why? I have no idea.
Probably because Levitate is considered an essential part of those Pokemon's design. I know it's inconsistent with stuff like Magnezone, Volcarona, etc., but if a Pokemon isn't given an ability other than Levitate, then it means that it's supposed to always float.
Yeah he actually gets a niche that way being the only special based set up dragon
But Flygons special movepool isn't exactly stellar.
Roost, Quiver Dance, Dragon Pulse, Earth Power. Seems like a neat moveset to me. It also has Hidden Power and Flamethrower/Heat Wave for coverage, as well as Signal Beam.
It's not amazing, I grant you, but Volcarona is an absolute monster even with just a recovery move, Quiver Dance, and two STAB attacks. With that moveset very few things could wall it, and those few things could be dealt with through HP.