If you upgraded to a business account (you need this to accept anything that's not a direct Paypal money transfer -- for instance, a credit card payment) - then you're going to incur this fee on every single transaction you ever receive at that account from this moment forward.
The only alternative is to create another account, and use that to accept non-CC payments, and just use the first one to accept the ones you're going to be charged for anyways. Sorry bout the bad news, but there's no going back on that first account.
Abuse flat-rate postage, especially going cross-country. Flat rate envelope will hold a large Priority video mailer, which holds 2 games inside (boxed or loose). Flat rate envelope is under $5 to anywhere in the US, and it's sturdy with the box inside. Order them both free at usps.com, shipped to your door.
Flat Rate box is under $10 and it ships up to 70 lbs in a 12"x9"x6" or so "wide shoebox" type volume. Holds up to 25 loose carts, one system with zapper + controller + AC + RF, or various other things. Great deal when shipping to Cali from Maine, or the equivalent.
usps.com also has Click-n-ship. You can configure it to debit your Paypal directly, and also click-through from your email Paypal payment reciept by scrolling to the bottom and hitting "print a shipping label." You'll need to set up your account, doesn't take long.
Priority mail is a bit more expensive sometimes, but you get free Delivery confirmation. I almost always opt for Priority over Parcel Post because 1. for close shipments, it's the same price (or cheaper) and quicker, and 2. for long distance shipments, the Flat Rate envelope/box will be cheaper than the Parcel Post option, and again - free delivery confirmation.
When using click-n-ship it will require delivery confirmation, but this is a good thing - since Paypal payments can get charged-back against you if the buyer claims something never came. Burden of proof is on you. It prints it right on the label, so no need to mess with those little forms.
Most post offices will let you drop off pre-labelled parcels at a spot set-aside for dropoffs - no waiting in line so long as you don't have foreign or other stuff to check out.
We'll talk more if you're doing international, but just remember - use the supplies at usps.com - make an account and get an order, so you always have the stuff on-hand.
As far as Media goes - I wouldn't mess with it. Just charge the customer enough to cover decent Priority shipping. It's quicker (less chance of low Detailed Seller Stars and poor feedback) and not a whole lot cheaper unless you're mailing huge lots of games.
For shipping single games, always go First Class Mail in a bubble mailer. If you're planning on mailing anywhere over 50 single games, then you should buy your bubble mailers online, I'll see if I can find the link for you if you need it. Otherwise just get a cheap package of them at Staples or wherever.
#0 bubble mailers will fit all NES cartridges (loose). Also, any CD-Roms in jewel cases or DVDs will fit in these perfectly.
#00 fits SNES cartridges
#000 fits N64, Game Boy, Genesis and most other portable games.
^those numbers are the universal classifications of bubble mailers, it's "what they're called."
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