I've used paypal, bank transfer, physically mailed check... i feel like there was some others.
Anyways, yes, paypal has issues due to fees. Some international bank transfers will incur fees and sometimes exchange rate issues, depending on whether you were specific about the currency you are paid in, which you should be specific. I often adjust my quote so paypal fees are considered, though I did not always do this. And when it is a larger project amount, that can be a problem, as it drastically changes the amount sometimes.
Creating a business account, and using it for bank transfers is ultimately the better way to go, but there are times when paypal is the right choice, or the faster choice, which may be relevant for certain deadline and scheduling issues.

Some clients will cover the paypal fees, some won't. Some prefer bank transfer, some prefer mailed checks.
Book publishers often send out checks, unless you are a repeat contractor with them, in which case they will set up a bank transfer on file.
In the end, you just have to work things out with clients, and find ways you are both satisfied with.