I think it depends on whether your local bottling facilities are owned by Coca-Cola Enterprises (about 80% of coke is) or Pepsi Bottling Group (about 50% of pepsi is).
Here in Maryland/Delaware, all the national chains/franchises pretty much use Coke (with the exception of the ones formerly owned by pepsi Taco Bell, KFC, LJS & Pizza Hut), with the exception of Arby's. So McD's, BK, IHop, Chili's, etc all use Coke. HOWEVER, all of the mom and pop restaurants pretty much use Pepsi. The reason being that there Coke is bottled by CCE and Pepsi is by a local bottler so I assume is cheaper. So this would depend on your area.
That being said, I think you'd be best getting Coke if you can. Coke also gives you Minute Maid products. It's fairly hard to mess up the mix on Coke products, meanwhile, Pepsi products seem to be frequently off flavor (syrup to water ratio). More people seem to prefer Coke (albeit by a slim margin). From what I've seen Pepsi drinkers will settle for Coke if that's all there is; however, Coke drinkers will never settle for Pepsi - when confronted by a Pepsi fountain they will choose Mt. Dew or Dr. Pepper instead. Not a big deal breaker though, as I've never seen someone storm out of restaurant, they will usually pick something else.
Definately do fountain drinks if you're going to do dine-in, but if you think most of your sales will be take out - you want to probably get your own cooler and stock both Pepsi & Coke, and both in bottles and cans. 20oz. bottles you're not going to make as much margin on as you have to sell for about $1.29-1.69, with a cost of around $1/ea. Cans can be had for about 25cent ea and you can sell for $0.50-$1 ea. You might be able to cheat and find the 16oz bottles of Coke/Pepsi for $0.45-0.75 ea and sell for $0.99-1.29. People do not like getting fountain drinks carryout as it is hard to carry bag of food, fountain drink, and try to open door of restaurant and fumble for keys to open door on car. (unless you have a drivethru)