I have no experience with Merc/Tohatsu/Nissan/'Rude stuff. All I know is Yamaha.
Yamaha's factory tanks are FAR superior to anything you can get from Academy. They are thicker low-perm material that does not swell or collapse. Speaking of the 3 gallon tanks exclusively, I have not had any feedback from their OE 6 gal tanks. I have a 3 gal tank. Cost me well over $100, and I work for a dealer and got 20% off retail. Reason I spent that money on a tank? Because I've had a Moeller and an Attwood (both from Academy). One of them BROKE during operation (running up river/smooth water, tank swelled due to pressure buildup and split right at the mold parting line). Spewed fuel all over the boat. Spoke with a manufacturer representative, they didn't offer anything but an apology. The other tank also broke at the mold parting line, that one while it was sitting in the boat and just a few drops of fuel in it. Both of them are the supposed EPA compliant tanks, which is all you can get now. The old tanks, if you can find them, have a traditional vent. While the idea of the vent is nice, if you combine it with today's "quality" fuel, the vent allows moisture to enter. The OE Yamaha 3 gal tank I have-so far I have not seen any moisture in it. Had it about 8 months (bought it Feb 2013). It is recalled due to the fuel line connector, but I like the round connector. I'll probably trade it in this winter so they'll quit sending me letters.
I know Yamaha's tanks are made by the same folks who make another brand, however, it's about the same as Sabre and John Deere. Made by same company, but totally different products, at least for a while anyway. Now all the JD stuff is basically garbage, IMO.
Fuel quality has changed. Used to be that you could let fuel sit in a vented container for an indefinite amount of time and it would be fine. Nowdays, fuel evaporates VERY quickly. When it evaporates, the remainder loses heat, which then causes condensation to form. Pretty soon you have WATER in the what's left of the fuel. Kind of like saltwater. Once it evaporates, it leaves behind the salts. Same for today's fuel. That's why I have been suggesting the new style Low-permeation fuel tanks, even though they cost more. I hate the price too just like everyone else does.