I'm not sure where you saw a product named "Mega 2560 Due". Certainly not in the Arduino Store. Some eBay, Amazon, etc. sellers of Arduino clones and derivatives spam their product titles with related keywords in hopes of getting more sales, but this also can lead to confusion.
There is no such thing as a 3.3 V Mega 2560. They are all 5 V.
Even though it has a similar header layout, the Due is a very different board from the Mega 2560. It uses a completely different microcontroller with a different architecture. The Due has much more processing power and memory than the Mega 2560. Just compare the "Tech Specs" on the product pages:
It's true that many of the accessories that are commonly used in Arduino projects are 5 V, and it does make things a bit more complicated to safely connect these to a 3.3 V board. On the other hand, many of the modern parts use 3.3 V logic, and thus are easy to use with a 3.3 V board.
I think the Mega 2560 is better for beginners, as it has been around a lot longer and thus has an amazing level of community support. You'll find many more libraries and tutorials that are compatible with the Mega than the Due (though many lots will work for either). The Due is great if you need the better processing power or memory for a demanding project.
As far as the selection of the controller is concerned based on the operating voltage. NOte that 5V supply controller can sometimes supports both logics that is 3V3 and 5v. The difference is you just have to apply different supply voltages for different logics. and with the 3V3 controller only 3V3 logic is available.
The logic is not the probelm if you are using the controller for simple applications. but if you are using the controller in the complex digital system then you need to make sure that what logic TTL or CMOS is mostly used in the system and then based on that information you select the controller.
This does not directly answer your question but I use a lot of Arduino Pro Micros which you can get in 3.3 and 5 Volts, I usually use the 3.3 Volt versions as many of the sensors operate at 3.3 V. Having the Arduino board and the sensors operate at the same voltage just makes life easier. Another advantage with the 3.3 V is they run at 8 MHz instead of 16 MHz, I like this as most of these boards end up in battery operated remote sensors so the reduced clock rate reduces power draw.