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MiniPCIe allows for adding wifi, network, storage (M.2) and other cards.

M.2 limit to only storage.

M.2 can be used for PCIe (including NVMe, wifi+bt, LTE modems, etc), SATA (storage only), or other weird stuff depending on the keying.

Afaik large share of embedded WiFi/BT and 3G/4G chips are USB ones?

m.2 can have USB lanes aswell

Aren't there WiFi and Bluetooth cards using the M.2 interface?

Yes. The A/E keys allow for PCIe and USB, among others. My Intel Wireless-AC 8265 WiFi+Bluetooth card is an M.2 22x30 card.