Having formerly managed a Gamestop, I can assure you the games are supposed to be on the shelf in alphabetical order. If they're not, that store probably either sucks and/or is lazy. There's usually a "Top Titles" section across the top, with a "Coming Soon" row as well, but by and large, the sections aren't arranged in any particular way other than by the alphabet.
Companies aren't paying money for better "shelf space" since the shelf space is different from store to store, and it would require countless hours just to determine the "prime" spots in each store. The marketing kit is what companies pay for, and those ads will find a spot in every store, regardless of layout.
The dedication you show to any particular console or company is inversely proportional to the number of times you have gotten laid. If you get laid enough, even if you prefer a certain brand, you just don't give enough of a shit to argue about it on the internet.