the main thing to think about is where are you getting your tune from? it doesnt matter which one you get if you are just using a ford voucher retune or one of the non-custom canned tunes that come on an sct or diablosport. the real gains from any intake are when it is paired with a tune that is custom for it. also, just to clear it up, the only CAI that I have seen that will work with any type of supercharger is the Steeda/FRPP one like this
even then it will only work with the saleen (its what comes in brenspeeds upgrade packages) and maybe the Roush M90. the only difference between the Steeda and the FRPP like in the picture is that some of the old Steeda ones had a MAF that was smaller so that it could be used without a tune, but I havent seen one of those for sell in a long time. really as long you buy one that is from a reputable brand (Steeda, FRPP, C&L, JLT, and couple others) and get a custom tune for it you will be happy. I picked my FRPP one because it is the same as the Steeda and they have never let me down with anything they have done on any of my previous mustangs. You can actually find it for around $150-$170 on ebay, then buy the steeda elbow for around $100 from one of the sponsors of this site.
All the being said, if you must choose between the Bullitt style FRPP CAI and the JLT, I would pick the JLT.