If it's an option for you, buy the console at Costco- my understanding is they have better return policies.
As for Gamestop's pricing- BotW is a bad example, as Nintendo doesn't like to drop prices on their flapship games. Even cart-only copies on Ebay still run $45. But yes- their pricing for used games can be very silly if the title's new or desirable. You'll do much better on last-games.
Gamestop's in an odd position, in that they're the only game retailer in town, so we forget to treat them like a retail chain. Do you pay full price for a pair of pants at Macy's? No, you wait for a sale! Did I pay $40 for God of War on PS4 a few months after it came out? No, I bought during a pro day sale for $20! It all works a lot better that way- Gamestop for sales & clearance, other places for big titles that don't drop in price like first party Nintendo.