Arduino has more digital I/O pins and 6-7 pins that can do analog output (via PWM). This new Arduino has even more pins and can do both 3.3V and 5V logic, though I fail to see the advantage of mixing those up. Overall, Arduino draws lower power too.

In any event, if you're looking for something with more pins, beaglebone black or olinuxino have them.

https://www.olimex.com/Products/OLinuXino/A20/A20-OLinuXIno-... (that one has 1GB of RAM, gigabit ethernet and SATA2 capable of running a small laptop HDD off the board's power)