It's not that shipping is crazy, it's that the profit margin on consoles only is very low. That's why you see N64 consoles only in the wild for $5 and still sitting there. Resellers know it is not worth the time and effort to buy it, clean it, test it, take pictures, list it and ship it. All of that for $5-$10 profit after fees and shipping? No way.
If you're looking to get the maximum price out of your lots, it won't be in reducing shipping. It should be about adding value.
Add a SMB / DH cart to your NES bundle so it sells faster / higher. Add 1 controller and a popular game to your N64 bundle for similar results (examples: Zelda OOT, Goldeneye, Super Mario 64, etc.) Those bundles still ship for the $10-$12 you've mentioned, yet they'll probably net you $30-$40 after fees and make it more worth your time.
Otherwise, there is very little demand for a console bundle that is not plug and play. People want to be able to play it the second they get it without additional purchases. You need to cater to that audience if you want to sell systems... that's the true market for this stuff.
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