Pokemon Go dev argues sponsored locations are more game-friendly than IAP
gamasutra.com
gamasutra.com
Like for example I remember when Gamestop offered download codes when people visited their shops to get a specific Pokemon in Pokemon X and Y, for example. That seems fine to me.
But if it gets to the point (as it often does), that company Pokestops are advertised from other Pokestops, or the screen gets completely taken over (think a website where the entire border of the site is an ad for one company) and there's autoplaying videos and they tell you to go to their place for REAL WORLD items (like Burger King says "Try our new Bacon Double Taco Whopper!"), then that will suck and I'll stop playing the game.
I'm already sick of dealing with it on websites, I don't want to deal with that while playing games too.
Ingress also had in-game items named after companies, but these items could drop from anywhere and were likely to be added to the game anyway. A couple examples of these are the SoftBank Ultra Link and the "MUFG" (Mitsubishi UFJ Financial Group) capsule.
I think the only time they had a commercial partnership that gave someone in particular an edge was when they introduced Ultra Strike items, which could initially only be obtained on some Motorola-branded Android devices. These can now be obtained on any device, though.
Given that it's the same team working on Pokemon Go, I think it's unlikely that they'll make things annoyingly intrusive or force you to go to specific Pokestops to get certain items.