Yeah this is something I'd kinda like to see.
I host a dedicated server, and me and my friends regular do cooperative megamek's versus hordes of bots. Excellent fun. What would make it better is some kind of campaign management. Being able to fire up scenarios from the command line (along with the bot) means i could knock up some scripts to generate content, fire up servers...mail friends their battle is ready. and potentially process the results on a leaderboard. But not possible :/ Sadly I'm not a java guy either
oh and just in case you just want to start a dedicated server and thats all you wanted its...
/usr/bin/java -jar MegaMek.jar -dedicated -port 2346 -password mytopsecretpassword