The main difference is the SRAM Red Quarq is sold with Yaw compatible chainrings which are what you'd want to use with the newest SRAM Red drivetrain that has the Yaw deraileur. It has one of the chainring bolts hidden behind the crank arm. The crank arms are branded "SRAM".

The ELSA powermeter has the same features as the RED Quarq (power balance, 1.5% accuracy, etc), but it comes with the standard Red Black 10 speed chainrings without a hidden bolt. This allows folks in the field to more easily change their chainrings. The crank arms are branded "Quarq".

In other words, I'd say base your decision on which drive train you are planning to use the powermeter with.

Mieke
Quarq Technology