When connecting to the server I get:
[INFO] Starting Minecraft server on 2001::6:25565
[INFO] Preparing level "world"
[INFO] Preparing start region for level 0
[INFO] Preparing spawn area: 73%
[INFO] Done (1,475s)! For help, type "help" or "?"
[INFO] /2001:0:0:0:0:0:0:6:52084 lost connection
[INFO] snacka3[/2001:0:0:0:0:0:0:6:52085] logged in with entity id 440 at (183.5, 65.0, 253.5)
I think it should read:
[INFO] Starting Minecraft server on [2001::6]:25565
[INFO] Preparing level "world"
[INFO] Preparing start region for level 0
[INFO] Preparing spawn area: 73%
[INFO] Done (1,475s)! For help, type "help" or "?"
[INFO] [2001::6]:52084 lost connection
[INFO] snacka3 [2001::6]:52085 logged in with entity id 440 at (183.5, 65.0, 253.5)
Related? MC-3776
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OK, I yield.
I have no problem to understand what the server says.
But in my heart I still think "[/2001:0:0:0:0:0:0:6:52085]" and "2001::6:25565" are two really strange syntax(es)
and that http://tools.ietf.org/html/rfc4291#section-2.2 has no notion of "port"

Of course does RFC 4291 not mention anything of ports (I did mention that because I felt that you had URIs and not IPv6 in mind)
Well, the brackets and the slash at [/2001:0:0:0:0:0:0:6:52085]
are strange, but 2001:0:0:0:0:0:0:6:52085
and 2001:::6:52085
are both valid IPv6 adresses.
IPv4 adresses are logged in the same strange way:
2013-04-01 12:10:29 [INFO] /127.0.0.1:56842 lost connection
2013-04-01 12:10:31 [INFO] Kumasasa[/127.0.0.1:56843] logged in with entity id 41 at ...
But... It's just a logfile...

BTW: RFC 2732: Format for Literal IPv6 Addresses in URL's (sic!) (The superfluous apostrophe was just quoted...)
Notation is correct, see http://tools.ietf.org/html/rfc4291#section-2.2
You mean the IPv6 encapsulation in URIs to separate the adress from the port like