Thats pretty hard to say.
A lot of people still use GWX (Grey Wolves Expansion). But you would need to install alot of additional mods to get it to a "modern" SH3 standard. It has a bit of "all" from the other megamods and is a great balance. I guess thats why most people still use this one.
If you need a good all in one package which is also beginner friendly I would recommend LSH3 (Living Silent Hunter 3
http://www.subsim.com/radioroom/showthread.php?t=220285). It has a lot of new ships and also has widescreen GUIs.
If you like eye candy and seeing and "participating" in historical events I would go with WAC 5 (
http://www.subsim.com/radioroom/showthread.php?t=233626).
If you want to be hardcore and play with a very good enemy AI but with less eye candy you should go with NYGM (
http://www.subsim.com/radioroom/showthread.php?t=139231).
All in all its up to personal taste and if you should try them all to see what fits your taste the best.
Here is also a short summary of the different megamods.
https://steamcommunity.com/sharedfil.../?id=315056037