How about upgrades, perhaps a shop for upgrades for something you can do yourself (like airstrikes or bombing runs). Perhaps a two player mode where 1 player defends and the other attacks (keys to summon a creature or build a tank to attack or to defend etc)
It's very difficult to improve on current tower defense games. I would say make it story based, in the present time. Possibly humans against aliens or something. Of course, have different types of towers and upgrades for each tower type. Finally, in the story mode, if you could, make some levels where you have a teammate building with you. There are 2 ways for that: 1) there is one path, and both the player and comp teammate build. Downside: if the player doesn't agree with the comp's decisions. 2) two paths, one for player and one for comp, but both share resources.
If you plan on doing a teammate level, I would suggest having upgrades/powerups that help you and your trammate. Or perhaps have a bonus system for both of you having upgrade towers.
I'll think of more later, and type them when I'm on my laptop and not my G1.
But....what about a whole new idea all together, thinking outside the box, making it new an interesting? Maybe combining a TD with another type of game?
You could combine tower defense with an RPG...it'd be hard but you could have levels of TD and of fighting, maybe it's in modern times, against uh aliens you move from major town to major town fighting with a character to move but then have the defense of the towns a TD. That'd be cool.