The story issues in Deadfire are a whole different topic, but the mechanical problems are all on Josh, and they're attributable to him trying to figure out what players want by analysing what they do, and drawing some of the wrong conclusions. There are improvements, mind -- for example related to visual clarity, and I don't thin dropping the party size to 5 was a bad call. But the attrition thing was a supremely bad call and it was driven by a particular bugaboo of his, namely his quixotic quest to eliminate degenerate strategies once and for all.
Same thing with the proliferation of classes and subclasses. It's just completely nuts and it's obvious his heart isn't in it. They're there because Josh thinks the fans want it because BG2 had a ridiculous proliferation of classes, kits, multi-classing, and dual-classing. He would've been much better off building all that into the classes based on the P1 system, as perks/talents/whatever you get to pick. He prefers classless systems anyway, so taking the game further in that direction would likely have helped.
IOW I'll go back to what I said earlier: it's clear his heart isn't in this anymore, and he needs to find it and listen to what it's saying. Then if it tells him not to make games anymore, do that. Or if it tells him to make the most autistically detailed historic Darklands tribute, then find a way to do that. Just stop pandering to an imaginary audience based on meticulous analysis of metrics, all that'll give is a soulless, empty husk of a game.