There's a good few reasons for it. Some of it is how some publishers gut the retail chain via exclusives in their own portals.
It's sadly incredibly hurtful when you can't offer the customer "every" version. It deflates hype and creates disappointment.
Ultimately, though, the biggest issue is that a lot of smaller shops don't have the buying/selling power to make orders large enough to meet certain minimum numbers.
Like, I don't sell first party Sony stuff, 'cause up until now, their local distribution partner demand I make minimum orders so large that I couldn't realistically expect to sell those amounts at street level – and said minimum amount is not just for units, but also cost, so with some products, I'd have to group things together and miss release dates or end up paying fullprice for stuff that has a sales/clearance price before I even get my stock.
If I had an online shop, sure, maybe I could do larger orders, but I want to focus on retail, cause of the community.
Anyway, tl;dr: If people want game stores to have a wider selection of niche stuff, be sure to use your local game store so they can grow in size and justify ordering the necessary amounts for things.
Also, don't skip buying small titles at retail cause the distributor does their own super special mega deluxe edition... double dip, if you have to, but preferably just drop the special edition and tell the publisher you want to support your local game store.
why cant they just sell video games in stores any more