This topic comes up quite frequently and it seems as though the top 3 most popular brands that people repower with, in no particular order, would be Yamaha, Suzuki and Mercury. The most popular choice seems to be Yamaha, though they're also likely going to be the most expensive as well as have the shortest warranty period at only 3 years. Suzuki is another good option, is usually the cheaper/cheapest option of the 3 and comes with a standard 5 year warranty. Mercury is usually the lightest option in the bunch, also comes with a 5 year standard warranty. Both Suzuki/Mercury have a 7 year promotion going on right now until the end of the month, though.
- 1999 Yamaha 250 ox66 25" shaft - 460 lbs per Google
- Yamaha F250 DEC 25" shaft - 551 lbs - 3 year warranty - MSRP per the Yamaha website is a minimum of $30k per motor for the digital/fly by wire controls
- Suzuki DF250AP Digital 25" shaft - 639 lbs - 5 year warranty / 7 year promotional warranty - Can be found in the high teen to low/mid $20k price range
- Mercury 250 FourStroke Series Digital 25" shaft - 527 lbs - 5 year warranty / 7 year promotional warranty - Can be found in the high teen to low/mid $20k price range as well
Which would bring me to what you're ultimately wanting, how much you're wanting to spend and so forth... if you're wanting to save as much weight and money as possible, then Mercury would likely be the better/best option. If you don't care about the additional weight, I think I would personally go with the Suzuki DF250AP if/when I were to ever repower my own boat. Both seem to be great motors with great service and come standard with a 5/7 year warranty, depending on if they're running their promotion or not. If you don't care about how much you spend, your warranty, etc, then Yamaha is always another option. Not trying to bash on any brand or anything like that, I honestly just think that Yamaha is quite a bit more money for what you get, which is a shorter warranty period and you could pay upwards of $10k+ per outboard more than going with Suzuki/Mercury. You could always spend a few thousand dollars less per motor with Yamaha if you wanted mechanical throttles, though it looks like their cheapest mechanical throttled F250 is $28k, and you're still paying more for a imo lower performance/optioned product comparatively. It really just depends on what you're looking for, how much you're wanting to spend, etc. Best bet imo would be to find a reputable dealer in your area that you trust, has great reviews and what their product availability/pricing is like. Good luck!