The Quake3 protocol has several weak points. In the past, when id was still having official releases, they would simply increase the protocol version, have a new point release and have their stuff fixed.
Indeed, we did not have that possibility until now because we were concerned with legacy support which is valid. On the other hand, there are the interests of standalone mod developers who will either need to abide by our restrictions of staying compatible and live with bugs, or either fix these bugs themselves. Why should we not fix this if we can?

I have prepared an initial patch which adds the new protocol with number 69, while legacy support for protocol 68 is still available. Both servers and clients are fully compatible. Servers should appear in the master server lists, too.

The support for the legacy protocol is completely disabled for standalone builds per default. For cases like openarena the cvar "oldprotocol" can be used to change the protocol version number that is recognized as legacy.

I have tested this kind of protocol separation for my EliteForce port and it works very well. I'd like to have this included as this fixes a long-standing vulnerability in the UDP connection code reported by Luigi Auriemma, and it will help me with the VoIP bugs that are still open on this bugtracker.