Check the post I made in your other thread before reading this one.
If you don't have a V.1/V.2 L96, then you won't be able to do any of the upgrades anyways. But, if you do have one of those versions, then read on.
Shorter barrels aren't good because there are always some problems with the bb exiting the muzzle, unless you're willing to ream the muzzle wider. Plus, longer barrels give an fps boost and increases range.
There are many people who like Prometheus barrels due to the 6.03 diameter, while I and also many others like 6.01 barrels. If you MUST get a 6.03, then the M16's length is the ONLY option you can go for. That means you must find a way to cover up the little bit of extra barrel sticking out, as mentioned before.
However, 6.01's are, in my opinion, better than 6.03's. The argument between 6.01's and 6.03's is a very theoretical one, and as of now, there isn't a definitive answer. If you decide that you want a 6.01, your choice in barrels is now MUCH more expanded.
There are several 6.01's out there that will work for the PDI hop up chamber (which is an AEG cut barrel).
The BEST inner barrel in the entire world is this one:
http://www.airsoftatlanta.com/Airsoft_PDI_Type_96_6_01_Barrel_495mm_p/66271.htm
If that's out of your price range, there is a second one. Same company, different metal (the only one I can find in stock anywhere, so it's overseas):
http://www.x-fire.org/etop/01+.html
Lastly, if neither of those sound appealing to you, Dwayne Dees can custom make you an inner barrel.
http://www.precisionairsoft.com/Articles.asp?ID=135
Dees is basically an airsoft legend when it comes to inner barrels. He makes arguably the best brass inner barrel out there, and once they break in, they're unstoppable. Just shoot him an email and ask him. I don't quite know if he'll do 6.03's, but I know he does 6.01's. Just specify that you want a 495 mm inner barrel with an AEG cut, and he'll cut you one. I think it'll be about $60-80.