The clock runs at 16MHz, not 20MHz, although this can be changed fairly easily. The documentation and even the text on the box is wrong when it states 20MHz. The clock runs off the internal oscillator instead of a crystal, not good if you need extremely high accuracy.
There are four hardware serial ports, only two of which are available with the Arduino core.
The program memory and dynamic memory (RAM) occupy a single address space, so there is no need for the use of special PROGMEM instructions, and the compiler will automatically store const values in program memory when possible, freeing up RAM.
Use of MCUdude's
MegaCoreX gives you a lot of flexibility, such as easily changing the clock frequency and allowing access to all the serial ports.