I agree that the Nexus War style of advancement (which has found some degree of mainstream exposure in Tabula Rasa) is a little dissatisfying, but it'd be really neat to have some differentiation between members of the same class in TH.
Maybe something more along the lines of talent points in WoW -- In WoW, a Holy Priest doesn't get an entirely different set of skills than a Shadow priest, but he gets passives that increase the effectiveness of certain skills, and very occasionally gets a skill that only Holy priests can use. Your choice of talent spec can make a HUGE difference in how the class plays.
What if, at different points in your hero's level advancement, you got some kind of, I dunno, Inspiration Point. You can spend 'em in your hideout, and at each stage, they give you some kind of choice. Like, when spend your first point as a Gadgeteer, you get a choice like
a) Spend some time messing around with the robotics kit you got as a gift in college and never played with, or
b) Flip through that pile of programming books you ended up with after the startup you used to work for went out of business.
Picking a) gives you a new skill, which is a buff that summons a robotic drone to follow you around and occasionally attacks things. Picking b) gives you a passive that lets you do something new and interesting with the code bits you've got laying around.
If you picked a), the next Inspiration point can be spent either outfitting your robot with an automated first-aid kit, so it also heals you in combat, or else giving it sharper sawblades or whatever. If you picked b), you get a choice that somehow alters the ways in which you can use computers further.
Elementalists could elect to spend an hour a) lighting matches and watching them burn out, or b) defrosting their freezer, which would determine a fire vs. ice path, and the second choice might branch it out into fire/earth, fire/air or ice/earth, ice/air.
Anyway. Not to degenerate too far into the user-created content realm, but it seems like some degree of customization would be a neat way to put in powerful skills without having to worry about power creep from people having ALL of them. And if new passives tended made one type of skill more powerful with a corresponding decrease in effectiveness of a different skill, then that's another avenue for balancing things out, too.