I'm sure ther are varied opinions. We went Miami to Marathon via Hawks Channel, then to Marco, on to Venice, then Fort Myers is a short hop.
We have done both several times. The lake route is about 40 mikes longer. Going around the bottom, (Florida bay), is nice also. We stop at Plantation Key, then follow the ICW until the "yacht navigation line). We stop at Everglades City next and enjoy the most beautiful 7 mile ride in from Indian Key. Next, if you can avoid low tide, the trip north through Goodland Pass is nice. You wind up in the Gulf north of Marco Island.
Don't forget about the five million crabpots around the Keys. Talk about having to steer...
I would think the weather would dictate the best route to take.
To Venice and then Fort Myers? That really was the scenic route.
I like going through the lake myself, and it gives everything a nice, freshwater cleaning on the way through. I read something that they're changing the lock hours, so you may want to check if you decide on that route.
One good reason to use the "yacht navigation channel" instead of going to Marathon and north is to avoid crab traps. The yacht nav. channel is the border of the Everglades National Park. They don't allow any traps in the park. No commercial fishing at all. A trouble free ride.