I think that a sequel should filter out what didn't work and build on what does. To completely depart from what you've already set up is ridiculous especially in an RTS where people might spend a very long time just adapting to the new system, you should just launch a new series for that. So, as you can probably guess, I'd say the better sequel from there is Starcraft 2.
Plus when you're being innovative there's always the chance you'll innovate a bloody stupid idea and trash a perfectly good game because you couldn't leave it the hell alone, naming no names here

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