The Cobb Intake setup utilizes the OEM lower airbox and both utilize a similar hardpipe intake arm setup. Between the two, I think the Cobb unit has better heat shielding properties because of its basically sticking a cone into that cavernous lower airbox and seals it- any true sealed airbox intake will be the more consistent performer. The Injen intake works great when the car is moving at speed and if you help seal up the heat shield better, or modify the injen unit further by rerouting the intake inlet further after relocating the airbox.
The Injen Intake, I think, will provide a louder "blow off valve" kind of noise and due to slightly less restriction might have slightly better tip-in response, but that's simply down to the inlet. If you want a Red intake I would probably go Injen. lol. Outside of that, the intake you choose is up to you, but between those two choices they're going to be fairly similar and I think I've given you a realistic idea of what to expect, having had the Injen intake on my car for a few months (I gave mine to a friend and it's on his Fiesta ST now) since I will need to produce Cobb's official "how to" vid for the intake.
Both are great products and will be a great compliment to an AccessPORT.