Class-based throttling: Currently the rules would allow ISPs to define certain classes or content and speed up or slow down traffic in those classes. Critics argue that not only would this almost guarantee the slower transfer of encrypted traffic (since it can't be read and hence classed),...
Critics are idiots. The packet type and transport metadata (upon which any efficient class-based packet prioritization system is built) of "encrypted" data is ... not encrypted. It can't be, because it would prevent the packet from making it from source to destination.
Deep packet inspection (wot would fail on encrypted packets) is undesirable as it requires scanning the whole payload every time.
No, the real problem with class-based throttling is that 90% of internet traffic falls into one class: HTTP/HTTPS, because sloppy web designers are pushing everything from binary file downloads to streaming video to VPN services over a single protocol designed specifically for text transfer*.
Putting, for example, file downloads back into FTP/FTPS/SFTP would not only allow them to be prioritized differently from HTTP/S more efficiently even when encrypted, but would allow for class-based optimizations within client and server as well. But that would require intelligent design.
* Or, more accurately, a single protocol ostensibly designed for text transfer, but which is actually just a hack of a hack of telnet.