I had a 40 HP 2006 Suzuki for four years with over 300 hours. Other than an initial wiring harness issue, the engine ran trouble free. The only issue was that I had to normally run the engine at 5,000 to 5,400 rpm to go 20 knots. The engine was so loud, I needed to use earplugs. It probably would not be a huge problem if people are riding in the cabin, but in the cockpit, I feel sorry for any passengers when you are running at a high speed. On the other hand, the engine was remarkably quiet at 2,000 rpm. So they are great for moving at hull speed. Finally, Suzuki 40's weigh more than other comparible engines becuase they use a timing chain, instead of a belt, and utilize a hydraulic chain tightening mechanism. Multiply this difference by a factor of two, and if you add a kicker -- that's more weight on your stern then with a similar configuration with Honda's or Yamaha's. Personally, despite what I stated, I loved the engine. At my marina, they used a 70 HP Suzuki for their shuttle, and had over 8,000 hours on her! The marina owner told me that all they ever did was basic maintenance and they had to change a starter once. What better endorsement could there be then that? Incidently, the 40 HP is EFI. I never ran into ethanol related issues. People with carbureted engines infrequently used had numerous issues at my marina. So whatever choice you make, whether it is a twin or single set-up, I recommend going with a choice that has electronic fuel injection. Suzuki, Honda, Yamaha -- they are all good engines. Stay away from carbureted engines, particularly in warm climates, unless you have a source for non-ethanol fuel, but that's my opinion.
Rich