Yes.. I too do not like HAT as a general-purpose solution. Its not impossible to really make an all-inclusive design, but I think its pretty hard, the form factor itself imposes a challenge.
First of all, lets call out a key thing, an official Pi HAT is a very specific thing, it has to conform to certain guidelines, including a specific EEPROM spec for auto-detection. Only then it can be called as HAT. Otherwise, we should just call it Addon board, with HAT's form factor (i.e. it sits on top).
The problem I see with stacking HATs are
1) The form factor becomes weird. You get a brick-shaped thing where pi connectors (HDMI, sd card slot etc ) are in one place.. now for exposing all PWM, outlet, inlet, ph probe you'll need connectors in another place. So if you conceptualize the end product, you have a brick-like thing with connectors popping up from multiple directions:-/ . I dont like that. I prefer the traditional rectangular shape with connectors spanning in one side only, this eases mounting and we know how to do brackets etc.. Its not impossible to get other designs, but they required significant design thinking/work.
2) The power delivery can get complicated, this typical perf board or pcb boards are less than 3A rated. The power requirements are kinda blocker for arbitrary stacking.