I am not sure that I understand what you are planning to build. From the Internet I see that a "10c Sim" is a flight simulation program. Therefore I assume you plan to build some hardware, like flight stick and throttle, to provide the necessary input to the PC on which this sim program runs.
The number of digital i/o and analog inputs you mention is not true for "each Arduino" but only for an Arduino Mega.
To expand the number of i/o pins you could add another Arduino, but this makes the programming (much) more complicated. You could set them up as master and slave, where the master tells the slave which output to perform and the slave tells the master which input came in. Or you can split-up the total system into two subsystems where each Arduino has his own responsibilities to handle it's part of the system. In order not to lose many i/o pins to the connection between both Arduino's, the connection between the two Arduino's has to be serial.
But there are better possibilities to extend the number of i/o-pins. IC's (chips) exist wit a serial input and a number of (parallel) i/o pins. A special case of this are the IC's working with I2C as the serial connection. Look at Google for "i2c port expander".