I'm not asking why you'd need a new transport protocol, that much is clear. The question is what is the disadvantage of building this new protocol on top of UDP, especially if you don't expect to work with middlebox developers to add special features for your new protocol.

The only thing I get from that document that answers this question to some extent is the extra overhead of the checksum field in UDP headers. In other places, they generally don't seem to actually discuss the option of building a QUIC-like transport, that is a transport-layer protocol that still exists on top of the UDP skeleton.