I think we have a terminology misunderstanding here. The address you're trying to "normalize" (fd12:ba74:4ba8:2e::3) is already normalized according to the article and the RFC (see http://tools.ietf.org/html/rfc5952#page-10 for the details), thus it is correct that python outputs it unchanged. It's java that applies some other, different, formatting. If that's the one you need, then by all means go with java.

Python approach is not normalizing all the formats, where Java approach does.
Example:
If I ask to normalize IP fd12:ba74:4ba8:2e::3, outputs are

Python: fd12:ba74:4ba8:2e::3
Java: fd12:ba74:4ba8:2e:0:0:0:3

Output by Java APIs seems following RFC.

normIP = java.net.InetAddress.getByName(IP).toString().substring(1)

Your problem is one of bash syntax. For unknown/untold reasons, you're trying to put a complex command in a variable for later execution, something that looks completely unnecessary to me here. If you insist on doing that, please read this page: http://mywiki.wooledge.org/BashFAQ/050 where the topic is covered in detail and at least use one of the methods described there. You should also get into the habit of using quotes around your variables (http://mywiki.wooledge.org/Quotes), and $() instead of backticks for command substitution.

I'd rewrite your code as follows:

#!/bin/bash
fill(){
 python2 -c "import socket; print socket.inet_ntop(socket.AF_INET6, socket.inet_pton(socket.AF_INET6, '${1}'))"
}

IP="0:0:0:0:0:FFFF:204.152.189.116"
norm_ip=$(fill "$IP")
echo "$norm_ip"

#!/bin/bash
fill(){
convert="python -c \"import socket; print socket.inet_ntop(socket.AF_INET6, socket.inet_pton(socket.AF_INET6, '${IP}'))\"`
}

IP="0:0:0:0:0:FFFF:204.152.189.116"
fill
echo "command: $convert"
norm_ip=`$convert`
echo $norm_ip

Execution of this gives:

command: python -c "import socket; print socket.inet_ntop(socket.AF_INET6, socket.inet_pton(socket.AF_INET6, '0:0:0:0:0:FFFF:204.152.189.116'))"

SyntaxError: EOL while scanning string literal