Edit: Sorry didn't notice the Suggestions Forum above when I made this post
You should lock which heroes' you have available per specific map, then on Higher level maps increase the amount of heroes you can put (So 1 for early levels, 2 for mid levels, and 3 for the late levels).
Make it so you can't start the first wave till the hero is placed into one of the tower spots instead of the hero tower automatically being placed, this lets you customize a strategy based on your hero location.
Have the "Hero Tower" mostly just focusing on backing up the hero.
For example a physical based hero's tower (like a Berserker) would fire weak arrows around the Berserker, increase the berserkers stats, throw nets at flying enemies near berserker bringing them to the ground, and/or effect how often the Berserker goes into "Rage" mode.
For a Ranger based hero tower, the tower can spawn 2 mini guards that flank the Ranger, the ranger can get upgrades to its attack and range, a "spread shot" upgrade that fires 3 arrows, and upgrades for the Rangers "gaurds"
Other ideas for hero towers:
Traps: Being able to make a "trap" near the hero tower that damages ground units as they walk through it, they can "wear out" after awhile/or after a certain number of enemies walk through them forcing you to place them again or just randomly reappear in the same spot after a few seconds. Floating Mines that damage air units that fly into them, that stay untill something crashes into them. Could also do ground traps that explode.
A Blizzard that damages and freezes enemies in place for a brief moment (for a Wizard Hero). A gust of wind what will push enemies back, unless frozen (long cooldown time)
An upgrade that lets the Hero and/or Tower do more damage to flying enemies.
An upgrade that will let the Hero throw small bombs.
An upgrade that lets the Hero do AoE damage.
A type of Wolf that can jump over melee units, They'll be considered flying at this moment which would be funny to see them jump into Air mines.
An enemy type that "divides" into smaller enemies when defeated, and agains when those smaller ones are defeated. (can make a superboss that is made of 4 of the best of these types)
A flying boss in an armored vehicle, who continues on foot after being shot down.
An enemy that can replicate itself, (copy has current health of original)
A fast enemy that "grows" armor as it goes along, increasing its armor and attack rating but decreasing its speed.
Enemies that can turn invisible for a short time thus not getting targeted by towers or soldiers.