Number one thing to consider when repowering- what brands are handles by your local dealer. There isn't a Honda marine dealer in our neck of the woods, which means anybody needing Honda motors, and later Honda service, has to go out of the area.
I would avoid Mercury. The Mercury motor is a Tohatsu / Nissan engine on a Mercury lower unit. They may be good runners, but they are not popular with the C-Dory crowd.
Evinrude- I love the E-Tec 90. Good weight, good power, clean running and lots of torque. I know some aren't fans, but we've sold a lot of 90's without any problems with the engines.
Suzuki- The new DF90 is light weight, has the offset powerhead for extra gearing and can turna bigger prop than some others. We have installed a few of the 70 /80 /90's on boats and been very impressed. The last 19A we sold had the DF90 and it was a good performer, quiet and good acceleration.
Yamaha- Dependable, good running, but the heaviest of the four stroke 90's. Shares its block with the F75, which is probably going to be phased out in favor of the new 70. The new 70 is worth consideration as it is incredible light and was designed to be a replacemenmt engine for 70 and 90 horse two strokes.
Honda- We sold a used 22 Cruiser with a Honda 90 EFI on it. We all felt that is was not as smooth as any of the product we sell, and frankly couldn't see what the big deal about Honda was. We've run boats with 150 Hondas as well, and agian weren't really impressed. They were certainly competant engines, but not outstanding. Honda would love for us to be a dealer, but we don't see where they have anything in their line that we don't already have in the lines we carry, and we think Suzuki or Yamaha are better products.
We sell Evinrude, Suzuki and Yamaha, so can talk about those brands with confidence. The rest is just my observations based on boats we have sold.
Bottom line- who sells what in your area.