Simplified systems =/= intuitive systems. The OP's aim seems to more closely resemble the latter. Removing absolute false choices does not simplify a system. It just puts up fewer (even if minor) roadblocks.
If the "combo" skills had reason to be used out of combo, and then we removed that ability, then such would impair or outright cripple gameplay surrounding those abilities. But there is no such reason. Each combo is in itself one decision, essentially one ability. There's nothing loss in making its controls follow its design.
Now, I'd rather each skill be usable separately with varying synergies that allow for various strategic "open" combos, but short of that, why reject an intuitive system for what's actually being given. Are we too in love with the concept that we're given multiple skills even while hesitant to have any additional thought or strategy expected of us as to make use of them? If combos work for you, that's the design. The rest is just making the UI actually fit, rather than hinting at something more and being unwilling to provide it -- almost with mocking contempt.
How is 1, 2, 3; 1, 4, 5; 1, 4, 6 any less mindless than 1, 1, 1; 1, 2, 1; 1, 2, 2?
I have no issue handling every key on my three bars. With my Caps turned into a Right Alt, it's even nearly comfortable. The issue is future proofing and, frankly, that the option is obvious given how the skills are currently treated in game. True Thrust is not a separate decision from Full Thrust. Once you've started the chain, you complete the chain. So how does it warrant 4 keys to do 1 function (pure DMG + 15s BotD)?
It's a matter of future-proofing. Unless SE wants to cut out even more skills that DO actually have tactical weight or decisions behind them, our bars are going to fill up, and the amount of binds will become uncomfortable to access all of—not in Stormblood, and, if they skimp on raw ability count, not even the expansion after. But it will happen. So why would you not take the opportunity to remove redundancies? Is Warrior made more interesting for having to use two different slots for Fell Cleave and Inner Beast (unless one wishes to macro them)?
In the brief example I gave, you go from 1-6 to 1 & 2 being used, for the exact SAME spread of abilities, and the SAME number of possible choices accessible at each juncture. How does taking up another 4 buttons at all times without them ever being usable at all times increase complexity? By your view, every Monk must already be mentally impaired, because (OH NO!!!) they can't actually flub 2/3s the amount of skills you can. And guess what? They at least have a skill that makes all their weaponskills simultaneously available. No one else does.
tl;dr
Why? Button bloat.