This is sort of an apples to oranges comparison. The question is which one can you drive and enjoy daily? Are you buying as an investment and occasional rider? Which one can you park anywhere and not worry who will door ding it and ruin the cars value with paint work and repair? Which one can you take out Sat night and play with without fear of breaking your investment? Where do you park the GT 500 on Sunday while you're in Wal Mart sweating bullets somebody will scratch the GT 500 in the parking lot? Would you drive the 500 daily and rack up miles killing the value of the car?
To answer a few of your questions: Cars are not an investment. You can drive anything on a daily basis depending on where you live as far as climate. I don't take my GT500 to WalMart. There are morons all over the country that will vandalize cars and they don't care what car you drive. And I stay home on Saturday night unless I'm working.
The OP asked which one would you pick? There isn't anything wrong with either choice. After owning eight other Mustangs since 1986, I felt like buying one that I would drive when I wanted to instead of when I had to drive it. That comes with working for over 40 years and at times, like now, having three jobs. The GT350 will be an interesting car to own. And someone else mentioned that the car would not be a comfortable daily ride. How do you know? I could drive my GT500 every day. It is comfortable to me. The GT350 will be as comfortable as you want to make it.
There are owners who modify and lower their suspension, install exhausts that violate local and state ordinances, and add horsepower by various means. Are these cars more comfortable after the mods? Most seem to think they are, or they have to say so to justify all of the money they just spent on the car. Taking a $35,000 Mustang GT and adding a supercharger and other mods will have a total cost in the neighborhood of $55,000 after the fact unless you do all of the work yourself. Not many can or will do this themselves. Another $5000 financed above this price will possibly get you the 2016 GT350.
And again, cars are not an investment. I would have had to buy my GT500, find somewhere to store it for 30+ years and never ever drive it and gamble on whether the car will be worth either $10,000 or $1,000,000. The other alternative is to drive it. Whether you have a V6, a GT, a GT500, Boss 302 or the upcoming GT350 the cars are meant to be driven. You buy what you can afford and drive it. After working for a while and increasing your income there are opportunities to purchase higher end cars. That's why you see old guys like me driving new GT500's, Vettes, etc. Don't be envious, look forward to it. Life is too short to worry about investing in a thing that you pump gasoline into. Just my $.02!
2014 Shelby GT500:Delivered 4/3/13, Black/Black stripes/Black interior, SVT Track Package, SVT Performance Package, JLT Oil Seperator, FRPP Resonator Delete, Syntha Max blue air filter, Revan Racing shifter bushing, Michelin PSS tires, Lloyd GT500 mats, and yes the stock Shelby seats.