As someone who uses both USPS.com and Paypal to ship things, I can say that I honestly don't know what you're talking about? First Class options are still on the USPS website. Are you possibly referring to the "First Class Large Envelope" option not being available to purchase shipping for online? The reason for that would be because they want to regulate the envelope size restrictions, but they still display it so people can calculate shipping for that option. And First Class Parcel is readily available. There are also Priority options that aren't flat-rate.

And Paypal doesn't charge any sort of service fees for printing shipping labels. I don't know any websites that do, so I'm curious as to which ones you've been using that might do that.