How to increase number of micro-controller inputs?
If you want a large number of sensors to record simultaneuosly, then one way is to have sensors that can be strobed, record their own value internally, then be polled by the central controller at leisure later. But that takes some degree of an intelligent sensor.

At the other end of the spectrum is a central controller with enough I/O to record them all at once. As you say, you will need very many pins.

An intermediate position is some sort of latchable storage, parallel to serial registers for instance, that can latch your sensors, and then be interrogated later by the controller. Easiest to regard this as input width expansion for your controller.

How simultaneous is needed? You could use a controller with DMA to execute a very fast poll.