If I had to break up transport protocol research into two main areas it would be research into TCP and research into other protocols. Since TCP has established itself as the leading protocol for the internet today, many researchers find success in changing TCP to fit certain needs (as can be seen in Data Center TCP or Scalable TCP).
Others tend to take a more daring approach and look at completely new protocols, which may seem like a fruitless task in terms of improving the Internet, but their ideas make more sense when they are applied to smaller networks (although they may still be large networks) that need specific functionality (such as enterprise networks). The only problem that researchers taking this stance face is that their protocol needs to be "TCP-Friendly."
TCP-Friendly refers to the fact that the new protocol is fair (in terms of bandwidth) when competing with a TCP connection. Vegas was criticized for being less aggressive than Reno, while BIC was criticized for being too aggressive. It seems that in order for the TCP protocol to be replaced form this point forward that the Internet itself will have to evolve so as to demand a new protocol. Such is the case with protocols like Scalable TCP, which may become more useful as high speed networks become more prominent.
As far as the transport layer goes, even though advances are made all the time, it seems as though the field is somewhat stagnant since we are too willing to submit to the current working protocol (TCP Reno in this case) and, although some protocols are better, no other currently available protocol is good enough for the world at large to want to incorporate it on a large scale.
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