If you choose limewire, chances are, that your changes won't live for long (for example they completely ignored the credence-project which could have eliminated spam:
http://credence-p2p.org ).
I chose contributing to Phex, because I can make a difference there and my ideas are welcome:
http://wiki.phex.org/Developers_Wanted
If Credence had been implemented in Phex, I'm quite sure, that it would have changed the way Gnutella works, but they chose LimeWire and went down, because their code wasn't included in LimeWire.
Phex on the other hand now includes features like download strategies (i.e. download rare parts first), which were done by a developer who joined the team as long as he had time for coding, and they are now very dear to advanced Phex users.
The only thing Phex doesn't want is multiple networks for the same purpose. That means: Only one network for word-based searches (gnutella search query), only one mechanism for downloading files (gnutella download mesh), but maybe some time a new mechanism for hash-based searches (for example a dht), because that's a different function which needs to be handled different from word-based searches.
(longer reasoning:
http://www.phex.org/wiki/index.php/T...e_p2p-networks )