Playing Brood War at high level requires you to know all the timings, all the builds and all the maps, which is also a lot of knowledge but your enemy probably knows all you do to, too. For example sensing drops is one very obvious marker of player skill, but why doesn't "map sense" in dota have anything to do with skill? How is being able to predict enemy movement not skill in any game?
If you scrapped and started over, you'd probably end up creating LoL. LoL might even be more balanced, I don't really know, but considering how much less complex it is it very well could be. But competitive LoL seems one of the most boring things out there, and I've been repeatedly told those games often boil down to lasthitting. But hey, that takes skill.
If you didn't create LoL, what would your game look like, then? It's easy to design one, so why don't you give some pointers? How do you make a game that is at least as interesting as dota, but isn't dota, but is more balanced than dota? Don't think it should take you more than few minutes to do better than mushroom-eating Icefrog did in 7 years (+ whatever the other devs and Valve staff did), so I'm all ears.
Anyway, I'm having hard time seeing how reflex and APM are better markers of skill than strategy and decision making, both of which derive from game knowledge and often require split-second decision. You increase your ability to punish your peripherals by practicing, which is also true for your strategic abilities.
Edit: Coincidentally, it didn't even take long for Brood War to get to any point. Story of Brood War was that it was from the beginning accepted as fairly balanced, and while I might recall incorrectly I don't think many balances change were made to it. Original SC is a different deal, though.