If I read correctly, the 1.4 version of Minecraft has the ability to detect server version and will refuse to connect to an older a different version. This makes it somewhat difficult for us regarding our multi-version support. These solutions come to mind, without much thinking them through. Let's discuss 
(A) We drop multi-version support altogether. We keep the architecture, because it makes version transitions easier, but we don't use it to support multiple protocols
(B) We let the server admin specify which version they want supported through an ini file, that version will be reported to the client. Multi-version support will be there in the background, but effectively will not be used other thanthat.
© We let the server admin specify multiple server ports and versions on each port. One single port will have one version, but there can be more versions supported simultaneously on different ports.
So Mojang decided that they want the players to need to be aware of the technical stuff, connecting to different ports etc., instead of the server working on the details and deciding about the support. Nice
(A) We drop multi-version support altogether. We keep the architecture, because it makes version transitions easier, but we don't use it to support multiple protocols
(B) We let the server admin specify which version they want supported through an ini file, that version will be reported to the client. Multi-version support will be there in the background, but effectively will not be used other thanthat.
© We let the server admin specify multiple server ports and versions on each port. One single port will have one version, but there can be more versions supported simultaneously on different ports.
So Mojang decided that they want the players to need to be aware of the technical stuff, connecting to different ports etc., instead of the server working on the details and deciding about the support. Nice