Stacks will always be a problem. But guess what? If you're a random and there's a stack on the other team, there's a stack on your team too. The system will virtually always do 3+2/3+2, 4+1/4+1, and so on. I've never seen 2+2+1 or 3+1+1 though I guess they can happen.
So I don't consider "well stacks could ban counters to their cheese" to be a valid argument. Yours can ban counters to your cheese just as easily as theirs can.
The problem is that DotA is balanced around captains mode and the drafting within it. Being able to ban problem heroes (whether they counter your draft or whether they're just plain bullshit/overpowered) is a core element in DotA's gameplay balance and the fact that they're doing ranked without the banning half of drafting is a little fucking ridiculous.
Like I said, compare regular CSGO queue to ranked CSGO queue. I don't like CS enough to draw parallels but I know they'll exist, because ranked queue is dramatically different from regular - it strives to emulate competitive CS (which is what the game is balanced around) as closely as is practical for a "6 random players are put together" system.