All true. However, I totally agree that this would be a fantastic system. (Note, not "app", it would definitely have to be a whole system: database+phone/tablet+interfaces to third party databases.) Not something one or two guys could cobble up in the garage, but I do see a market for it. I think it's ahead of the curve, get on it now and by the time the stores realize it could bring them more sales, it will be ready to sell. You're right that right now the stores have no incentive to work with this kind of scheme because it's all about foot traffic and impulse buying for them. I think the way to counter that would be if the software brought them measurably more sales than impulse buying.
The other issue I thought of when I read the idea description was somehow getting the items sorted into aisle order for each store. Ideally each chain would have to number or otherwise order their products in the way most people walk through their stores - which is also against their impulse buying motivation, so not likely to happen soon. Less ideal but workable would be to have a team of key users volunteer to create and maintain a some kind of sorted list for the stores they shop in that can be used by the whole userbase. This would be occasionally defeated and have to be redone when the stores rearrange/remodel their layouts, as they do from time to time.
Generating a list of standard list items is easy, nearly everybody buys milk, so the list would say "milk". You could add a feature if you want to let them choose a specific brand and/or size. It would also be good to allow the user to de-select items from the standard list: "My whole family is lactose intolerant so we never buy milk. Zap it."
I can see this being implemented with SQL Server on the backend, Javascript and jquery on the front (jquery mobile rocks for iphone/ipads). After you build enough of it to make a nice demo, maybe it could be marketed to one of the more forward-thinking stores like Wegmans or Whole Foods to encourage a partnership. Get one on board, make it successful, and then others will want to join. (Or build their own, but that's okay too.)