If not designed very carefully, though, it can reduce the user's ability to view things as they like them. With the current status quo of mailservers not handling message threading and such, I can choose a client that handles it how I want. If the server is doing it, it had better either do it how I want it, or provide some way to customize what it's doing.
(For example, I don't like gmail's flat "conversation" view; I much prefer a "threaded conversation" view, like classic Usenet readers, or HN discussions.)
reMAP claims to treat conversations as first class objects. Given suitable APIs on top, I think you could build different views on different email clients.
I think what is meant by a new protocol and server innovation is a change in the data model. I do not believe they are going to dictate views.
(For example, I don't like gmail's flat "conversation" view; I much prefer a "threaded conversation" view, like classic Usenet readers, or HN discussions.)