It's taken me 7-years and I'm still learning but I view the naval rules/model in (M)WiF as most elegant and one that plays and/or produces historically reasonably results. It also rightfully punishes a player who does things that aren't tactically sound such as sending out surface fleets without proper air cover into sea areas where their enemy has air.
I found out the hard way that you don't send invading and/or transport task forces into areas where you don't have adequate air protection. In fact, I've found that air superiority, better yet supremacy, is a prerequire to successful invasions and, as significantly, successful maintaining of beachheads once one gets ashore.
Though some of these lesson can be learned playing solo, I really learned them the hard way playing against a more experienced opponent.
Not really meaning too, but in my "By the Numbers" game I just finished a two round (or possibly two day) battle in the China Sea where a small 3 carrier USN task force opposed by a massive IJN carrier and battleship task force managed to sink 1.4 million tons of Japanese shipping, sink 3 IJN aircraft carriers and a NAV air flotilla. In exchange, the USN lost the CV Wasp and saw the CV Yorktown and a CA damaged. This battle took place in Jul/Aug 1942. While the details vary, does this naval battle sound remotely like anything that might have happened in 1942? Honestly, I didn't intend to recreate any historical type carrier battle. It just happened in my play. You'll be able to read about it when I post the combat logs in my AAR after this current turn ends (hopefully) in a few days.
One thing about the naval model in (M)WiF that use to bother me was sub warfare. Though while the mechanics aren't exactly correct (i.e., sending CAs and BBs out hunting for subs), the results of the sub encounters are (I believe). Throughout the course of a game you'll see scores of convoys sunk by subs and in return you'll see sub groups damaged/sunk and a hand full number of "escorting" CVs damaged/sunk and patrolling CAs damaged/sunk. The sub battle is where I feel the results make sense but the details of how one gets there takes some liberties.