Another aspect of cost is the resale value of your motor. Will E-TECs have better or worse resale value than a 4-stroke outboard? If you're OK with some guesstimating, how about this train of thought:

If you go out on the Internet and look at places like Ed's Marine (which is a sort of notorious Internet Outboard merchant, sells Evinrude and Yamaha), a 2008 E-TEC 90 20" shaft runs around $7300. The 2008 Yamaha F90 20" shaft runs around $6200. There aren't any details on the exact configuration, but let's assume they are both electric-start, power trim and tilt.

If you look at the NADA website, which contains used boat and motor data, and look up used outboard prices, a 2005 E-TEC 90 has an average retail value of around $5800. A 2005 F90 has an average retail value of $5300. These are national averages of purchase prices, not trade-in value. So regional biases are not taken into account in the price, and don't expect to get these prices when you trade in the motor. But that's about the best I can come up with for estimating depreciation of the motors.

If you use the above trends and project a flat rate depreciation, it looks like the E-TEC would be worth $2300 in the year 2013, and the F90 would be around $3200 in 2013. Both of these numbers are probably too low, as depreciation curves typically flatten out over time (think about your new car). But again, since there's no actual data, we'll use this as a "best guess".

Soooo....The E-TEC depreciates (7300 - 2300) = $5000 in 10 years, the F90 depreciates (6200 - 3200) = $3000 in 10 years. So the E-TEC depreciates $2000 more.

As we said a second ago, this is ony a gross estimate. as more data becomes available, we'll update this number.