I also got Agent Analyst to work with ArcGIS 10.2 (at least so far). I had to perform the steps noted above, but given that it was a bit confusing with some of the responses I will summarize here:
Create Refresh.exe.config file with a text editor and save it along with Refresh.exe (typically in C:\Repast 3\Agent Analyst\Refresh). The Refresh.exe.config contents will be identical to the contents of the configuration file described here ("Update 2"): ArcGIS 10.1 using Repast's Agent Analyst Extension - refresh.exe does not work but you must replace newVersion="10.1.0.0" with newVersion="10.2.0.0".
As noted above, edit the agent_analyst.bat and agent_analyst_run.bat files in the installation folder (C:\Repast 3\Agent Analyst) so that the folder paths contain Desktop10.2 in the folder path strings:
rem set ARC_JAVA="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\java"
rem set ARC_JAVAW="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\javaw"
rem set ARCOBJECTS_JAR="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\lib\arcobjects.jar"
Then, edit your Environment Variables to make sure that ARC_JAVA, ARC_JAVAW, and ARCOBJECTS_JAR have a fully specified path entered for each variable (like what is in the .bat files above).
Then, in my Environment Variables, I had to move ARC_JAVA (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\java), ARC_JAVAW (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\javaw), ARCOBJECTS_JAR (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\lib\arcobjects.jar), AGENT_ANALYST (C:\Repast 3\Agent Analyst), and AGENT_ANALYST_VOL (C:) from my User Variables to my System Variables. Depending on your situation, I foresee that some people may not need to do this. If you install software and manage your system with a separate ADMIN account, then I think you will need to do this...I had to do so to get it to work.
Finally, make sure you restart your system and open a fresh ArcGIS session...
I'm new to Agent Analyst so I don't know if there will be other issues down the road, but now I am at least able to see the Agent Analyst user interface when adding a new tool so it appears that everything is working well so far.