Arguments against Ayton mostly have nothing to do with Ayton himself, but where the NBA game is and the positional value.
On offense, post ups, even from the most dominant bigs in the league, are just worse expected value plays than an average player shooting a 3. You'd rather have your backup wing who shoots 34% from 3 shoot than an Embiid psotup (.97 PPP on post-ups). Bigs that stretch are great... but then why play a center at all? Why not just play a PF or big wing (Horford, et al) at the 5?
On defense, most centers don't allow you to run switching schemes. Also, the prevalence of stretch bigs means they're likely pulling your center away from the rim anyways. So, again, why play a center at all? In this draft in particular, JJJ has the best ability to move and guard in space.
This trend has created a glut of cheap centers that can all give you the same things that have a use: rebounding, rim running, rim protection, and stretching the floor.
Why draft Ayton #1 overall when you can get Baynes for $4 million?