As stated in several places, developers' aim in aMule project is to create the best client for the existing ed2k protocol.
So I am quite happy they don't introduce any "innovation" in how the protocol is handled, because that would mean creating a restricted alternate network of users of the new protocol. That's also why they don't include in the tree some "extreme" mods...
The fact that some servers decided to allow some functions (search) only to obfuscated clients, and that a lot of eMule users are activating their "obfuscate connections only" option is quite arbitrary and souldn't have happened.
The "don't ask" list is of course a right thing, in order to avoid a flood of unnecessary requests. As you see, when something is really needed, the devs take the necessary steps.
And, of course, aMule is full of innovations, only not in in the protocol section. Look at the daemon, the remote GUI and so on...