Greetings folks. I just finished my first successful Arduino Uno project (engine control module for a diesel generator). I’m moving on to a more ambitious project that requires a lot of I/O. I don’t know if I should be using the Mega or the Due. Same number of I/O pins, same price, what am I missing? The most intensive computing the project will be dealing with is a fingerprint scanner - am I better off with a 32 bit machine for that? How do I know if I need an 8 bit or 32 bit processor in general? Sorry, I’m a nube.
The critical difference between them for your purposes is that the Due is 3V3. If that's ok, then the Due is more capable. Fingerprint scanners usually do all the heavy lifting themselves though, so you don't need extra computing power to use them.
Curiously, while I've seen many many posts here about using the Mega, I don't ever recall seeing one mentioning the Due. I've used one in a project, it was fine, but never had a need to post about it - perhaps its predominant use is by folks who have a bit more experience and aren't asking questions here.
Lack of frequent mention here could be because the Due is more expensive than the Mega.
OP, if you used any timers or processor specific code for the Uno, it will port more easily to the Mega because it has a more similar internal architecture.
And on the point of cost, it would be perhaps more appropriate to use a Nano and some port expanders.
I thought the Mega and Due were essentially the same price...
el_jefe_george:
I thought the Mega and Due were essentially the same price...
Apparently they are now. I don't think that was always the case.
So it seems. I might just be tempted to buy a Due to play with sometime.
In regard to the OP, you could buy two Nanos and four port expanders, that is enough to do the job twice over, for the price of the Due. 
el_jefe_george:
I don’t know if I should be using the Mega or the Due. Same number of I/O pins, same price, what am I missing? The most intensive computing the project will be dealing with is a fingerprint scanner - am I better off with a 32 bit machine for that?
They are about the same price.
The DUE is 3.3V logic of course, which means for some people its a better match for modern electronics.