i know you were thinking about this andy so heres what i've came up with and ill use the Hitman as my Base Example
Basic of this concept:
Level 25 , 50, 75 , 99 (max exp) The tower Can evolve to a new 'tier' (purple towers must be 99 max exp)
Upgraded Tiers of Towers Cannot Drop.
For this there would be a new 'tier' of tower color (Orange!!!) not attainable Via Drops!
Tower - Gem Color - Level
Hitman White 1-24
Sniper Blue 25-49
Assassin Yellow 50-74
Deadshot Purple 75-99
Dot ORANGE 99 max exp
Now you see the Upgrade order, Now if we are going to just have them Evolve they evolve when hitting the next checkpoint,
If upgrading they can keep lvling past checkpoints but cannot skip a tier (hitman lvl 50 cannot just go straight to assassin)
ORANGE TIER !!! - These towers Evolved or Upgraded you MUST have to complete some kind of special objective designed specifically for that Tower set to unlock the god tier (orange) and be available to upgrade or evolve into.
For the Hitman Tree of towers i would say Achieving a crit of a certain multitude.
As for skills well with the Hitmans its hard to change it around, but possibly with each Tier upgrade Add more Crit Damage to the bonus, and on the Purple tier give him another ability, and God tier Upgrade both of those abilties more!
White -25% crit chance/damage
Blue 25% crit chance 35% crit damage
Yellow 25% crit chance 75% crit damage
Purple - 25% crit chance 150% crit damage +1 multi crit , insert second skill here
ORANGEE!!! - 25% crit chance , 250% crit damage +2 multi crit , insert second skill here