Ender trophy can be used to TP across wall protection
Squid trophy can be used for placing water in the nether

Could you address those or add configuration so we don't have to disable all trophies or use plugins?

Also, for the record, metadata won't show up until you reconnect to the server, probably a client/server sync issue.

Squids: fixed in snapshot for some time
Endermen: now shots enderpearls. It's probably exploitable in some other way...

Can't reproduce sync issues, there is some lag, but trophy always shows in less than second.