I'd like to see ultimate skills become sub-classes that significantly change how a build is played, but not be required to be taken. Also to have their own (small) skill trees to further enhance the sub-class taken.
If you don't take a sub-class, you could then further enhance your base build from the skill trees you already have access to... Or perhaps a real "mastery" tab or high level skill in your current tree.
ex. Blink has no cooldown but stun removed > Blink deals 100% Weapon damage > Blink stuns for 0.1 second > Blink deals 300% weapon damage
ex. Not taking ultimate/sub-class skill > Ways improved 20% multiplicative per hard point. (high level required passive skill)
Balancing required, but that'd be my idea in a nutshell. To take it further, perhaps the ultimate skills would require a rare item drop to allocate, or during hell progression from Act bosses.