I look at it this way.. what car suits you and your style.. Because that's all it's about..styling
You can go to damn near any dealership and get invoice pricing, it may take a few walks to the managers desk but it'll happen. Believe me, dealerships are built to move metal not to hoard cars. Most people are just too scared to ask.
As far as both of these cars go let me ask you this. Are you going to gut the car the day you get it? If so get the car that's the cheapest and with the least options..Scion FRS
Or are you going to mildly mod this thing till the next gotta have it car comes out, only to trade in your FRS/BRZ.
Do you think that the econo FRS w/o heated seats, NAV, HID's, Keyless entry, Dual zone climate control, lighted vanity mirrors, etc...etc.. will be worth as much as a Limited Model BRZ?
Do you really think you'll keep this car more than 5 years? The average for the US is 57months of ownership until they buy something else.
We all know buying and modding cars is never going to make you money, but at least spend it wisely where and when you can. The FRS has it's unique niche just like the BRZ, figure out which one suits you and go for it.
Personally I like the creature comforts of the BRZ Limited and will likely swing that way. I mean c'mon who doesn't like their ass all toasty warm in the middle of winter!!