USB as a local bus in an embedded system
What you are looking at is a problem I like to call bus hierarchy.

You have high speed devices that need a fast low-latency path to the CPU (like the LTE modem) and slow devices like the temperature sensor. Connecting a full fledged LTE modem over I2C will seriously bottleneck the system. And connecting a temperature sensor on USB is a serious overkill. You need to prioritize.

What devices are to be accessed most often? Which ones need to respond quickly? And which don't need that much bandwidth?

Feel free to edit your question.



Edit:

USB may not be such an overkill after all. Only in the latest versions of it (2.0, 3.0) it has gotten the notion of being targeted to fast peripherals only. Before that, it was simply a Universal Serial Bus.

This doesn't change anything on the fact that it's implementation cost is very often too high.