NeoLoader has connection encryption option for BitTorrent but not for eD2k/eMule (it offers only protocol obfuscation).
If I remember correctly, Ekliptor's eMule Applejuice mod had options for protocol encryption too (AES).
Why not add that feature to NeoLoader too? It would significantly improve user's privacy (although not anonymity) and prevent MITM attacks. With ever increasing hostility against P2P sharing this feature would be very important.
If David and Ekliptor decide to implement it (I certainly hope they will), maybe it would be a good idea to make it so that it can be compatible with Applejuice (in order to maximize potential number of users).