Another vote for Total Annihilation.
I understand that the Commander in TA is meant to be the answer to the tank-rush tactic.
Also, if your Commander dies, if you have been playing effectively, really it should only take out a small portion of (one of) your base(s)

On the issue of super weapons, TA is littered with them. What I noticed amongst my friends is they'd go straight for the LRPC or nukes without building a proper offense or defense, and would thus usually get steamrolled. So to make games more interesting, we'd ban all long range super weapons.
An even more interesting strategy was to ban all units above level one. As a result, the number of units fighting was epic. The battle lasted several hours and kills on each side racked up in the thousands.

Cheers