Multiple sensors and control with microcontrollor
You basically have two choices.


Select a more capable controller device that has the functionality and memory you need.


or


As you intimated, break up the system to use multiple controllers.


The latter of course requires a bit more development and is harder to maintain, but it does buy you the ability to modularize the design so one micro can do one job really well as opposed to sharing resources in a big single device. Once that sub-system works, you can rely on it to continue to do so when you add different micros for other sub-systems.

You may not need one micro per sensor though. Consider grouping "like" functions into separate micros, if they fit.

If you go the multi-micro way you also have to come up with some form of a communication protocol between those and whatever is acting as the supervisor device. 

That could be I2C or some other true communication method. It could be as simple as a few logic lines to force the sub-ordinate processor to enter some state or do some task, with reciprocal return signals or interrupts. It really depends on the functionality required.

Whether you make up your own board, or stack a deck of Arduinos is up to you. There is some investment required if you go the custom route, with a definite possibility of having to go round a few design loops. 

However it also sounds like you probably have a tight space limitation so a big stack of Arduinos may be out of the question. However, if you want to stick to that micro, the stack would probably be the best bet for the initial proof of concept development. Once you prove the system works, then you can think about tight integration.