wizdum:
The pros would be cost savings and space savings. You can use the Arduino to develop your project, then get an atemga 168 for $3.33, load your code on it, and only add in the parts you need for your project.
For example, this is a board I made for my airsoft props:
http://nightscapetech.com/images/stories/bombprop/thumb/Bomb_Prop_PCB_diagram.jpg
It has the same basic functionality of an arduino, but only has headers for the pins I need, and lacks a USB to serial adapter since I don't need one for my project. That board, including PCB printing costs (which you wouldn't necessarily need), connectors, and a relay, costs me about $20.
Well that's quite a good looking circuit
Thanks for your help, cost saving is an important target of my project! 
GoForSmoke:
I think you have some learning curve before you build anything final. Reason being, the view from higher up will benefit your approach and designs greatly. And if you can nail cap sense down then you can make really neat surface-touch switches.
The legs on the ATmega chips are almost all I/O pins. Some have hardware support to do specialized functions -if you want-. Here is the pinout for the 168 chip (100% same as 328 chip) and Arduino:
http://arduino.cc/en/Hacking/Atmega168Hardware
The through-hole DIP chips plug right into breadboards or sockets. You can solder to the legs of a socket and then plug the chip in without fear of burning it up and confidence you can replace it.
How many ways you could go? Run everything from one chip or make a modular system that you can add pieces to?
The pros are lower end cost, expandability, possibility to sell parts to others in the community. BTW, I'm part of the FS community since 98 (at the old Delphi FSF) but different sims. If I can't shoot, it's not enough!
Have you seen the Leo Bodnar chip/devices? And some of the other simpit devices? Not real cheap but very polished and the work is done.
http://www.leobodnar.com/
What you get out of making your own is knowing how to make your own as you want. Keep that in mind when you have spent way more time than you ever thought you would -- what you get is more than the finished project. And here's a warning: Arduino can be as addictive as any flight sim made.
I DO have a learning curve indeed
I came up with the idea of using Arduino while looking for something capable of keeping the price low and the result as good as possibile. It's been a few weeks since I started to learn how to use Arduino and I still have a lot to know, and that's why, in my first post, I told I would show up in a couple of weeks, maybe some months
I wrote this post just to know if what I was trying to accomplish is possibile, so now I'm going to take care of the techincal part of the job. Again thank you very much for your help, I can be sure I will ask many other questions :).
On the other hand, a bit OT, what simulator do you fly with?