Faster CPU, and two of them. Note that the A7 is not amazingly faster (maybe 2x) than the ARM11 in the RPi, but it's more up to date (ARMv7 instead of the very old ARMv6) - and two of them does help a lot.
Slower GPU. The RPi uses a very advanced SoC in terms of GPU. The ARM11 is actually just a microcontroller for the GPU. The SoC was aimed at video applications, and is pretty darned amazing, for the price.
1GB RAM instead of 512MB.
4GB of flash storage, instead of none. Not to be sniffed at, but most people would just stick a fast SD card in anyway.
SATA support, versus no SATA support.
Open form factor, versus custom. Two boards (SoC board, EOMA68 I/O board) versus one board. Higher cost.
No software ecosystem versus an ecosystem of 2 million sold devices.