ESP is cheap and good enough for a lot of things...but there are plenty of projects where we need something smaller, lighter, faster, more power efficient, etc. If I don't need WiFi, why have it sucking up battery? Most (nearly all) of the projects we do use other long range wireless protocols. WiFi is just nice for prototyping. There are lots and lots of reasons to move from one board to another or to build your own.

As far as MicroPython goes, same thing. It's great for prototyping, but it's still somewhat hackey, slow, not that memory efficient. It doesn't need to be for its use case...but for production ready sensors I need to be sure to work the best they can off the shelf, I'm gonna write that in C/C++ or most likely Rust (if there is an LLVM backend for the chipset).