I researched this myself on other forums and based on independently verified results the E-Tecs use significantly more fuel ( like 3 gph more at cruise with twin 225 hp E-Tecs ), the two stroke oil is outrageously expensive ( $ 40 a gallon for the XD-100 ), they cost more to purchase new than some four strokes ( like Suzuki ), and their resale is just horrible.
The# 1 Wellcraft dealer in the entire country, Sundance Marine in Ft Lauderdale, just recently told me the only 2007 leftover models they still have in stock all have E-Tecs on them. On a saltwater fishing boat they are very hard to sell, either new or used.
They have a beautiful new 2007 Wellcraft 35' Scarab thats been for sale for nearly three years and the only reason they can't sell it is because it has triple E-Tec 250's on it. They have drastically marked it down to $ 115,000, a truly unbeliably low price, yet it still won't sell.
If at all possible put some four strokes on it and learn to change the oil yourself, its easy and you'll save ALOT of money overall.