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Are you comparing the Mercury engines that had the power head supplied by Yamaha? If so, I would say the new Mercury "FourStroke" is better in that it does not have the occasional carburetor fouling issue reported by some owners. The culprit with the fouling was sporadic use and very small passages.
I am not clear what "issues" you are referring to. E-Tec had some initial issues with some motors when introduced. A number of knowledgeable people say the number/severity was smaller than most new generation introductions. I have not read of any E-Tec issues in a long time.
Everyone I know with E Tecs LOVE THEM and have been problem free. Most of those people own 90hp motors. If I where to get a motor for a Whaler Today it would be an E Tec. Hands Down.
Are you still looking for a 90hp Merc? I know of one with zero hours carb'd Merc and it has been sitting in a friend's garage now for a couple years. He bought it new and was going to put it on his mischief but he just sold the boat and wants to get rid of motor. He is in Newark Delaware which is very close to you. If you are interested PM me I will give you his contact info.
the new etechs are the best engine out there, mercury is heavier more maintence worse on gas then etechs, etechs are the best motor out right now but they r 2strk