Maybe it’s different depending on what you sell (the value, number of items, etc.), but I don’t find eBay’s fees (or PayPal’s) to be complicated. However, I do NOT have an “eBay store” - I’m just an individual seller with 300+ sales over the past 5 years, probably.
eBay takes a 10% cut of the final selling price. The final selling price is the sum of the winning bid (or Buy It Now price / accepted best offer) and any shipping charge the seller has indicated in the listing. I haven’t paid a listing fee or image storage fee in years and years. (There are, of course, “upgraded” listings - i.e., listings with bold text, etc., that you can pay extra for; I never do.)
PayPal takes 2.9% (of the final selling price) + $0.30 per transaction. This can really eat into profits when selling small items because that $0.30 is a flat fee.
As beowulff said, ship to the address associated with their PayPal address. Do NOT ship to any other address. When you sell an item, you should receive an email from eBay or PayPal (I don’t recall which, and it isn’t really important) with a link to ship the item. You pay for the shipping cost through PayPal and print it at home.
You do not NEED to use this label - this label, by default, includes tracking. I frequently sell trading cards and just ship them in a thin, hard plastic case and put them in an envelope with a stamp, no tracking.
That leads to:
Dishonest buyers.
It does boil down to reputation (again, as beowulff said), but if you DON’T have tracking that shows it was delivered, you (the seller) will be responsible for a full refund. (In ~300 sales, I’ve had 2 people say it wasn’t delivered. Dishonest? Actually lost in the mail? I don’t know, of course, but the money I save by shipping a $10 card in an envelope with a $0.49 stamp vs. $2.60 for tracking is greater than writing off these couple losses.)
eBay does tend to side with the buyer, unfortunately. They do take into account reputation, history, and obviously tracking information.
I’ve also heard PayPal tends to side with the buyer. The only interaction I’ve had with PayPal (where the buyer did a chargeback, claiming I sold him a counterfeit card), they were great - they went to bat for me vs. the credit card company and ultimately, the credit card company reversed the chargeback (meaning I got to keep the money that was originally paid to me.)
There are a lot of horror stories about eBay, but I find the fees to be reasonable (compared to other platforms for selling collectible trading cards, anyway) and their customer service to be middling (but not needed very often).