You are right, it is all required to be checked and replaced if necessary. You do have a hell of a dealer if he was willing to drop the lower unit to check the water pump and do all the other required checks for only 50 bucks along with pulling the thermostats to check, which would, at the least, require new gaskets for the lower unit and thermostats.
I'm not trying to get into a pissing match with anyone over this. It seems to me the biggest "fan boys" are the etec guys. I am willing to concede they are good motors but they do have their drawbacks just like every other motor. Just google etec fouling spark plugs and see how many results come up. What happens (again straight from the manufacturer) is that when you run above the 2000 rpm mark but just barely there is some sort of bypass in the cooling system. Basically it runs much colder than it should if you consistently run it in that 2000-2500 rpm range. This causes the cylinders to not get hot enough and plugs to foul.
On cost of ownership:
Here's a great third party resource below. They based their numbers on the services and what is recommended for all. Before you cry foul when you look at your they include all of the "check and replace if necessary items" as part of the service and use base rates for labor. The service costs on the Mercury are a little higher than the estimates I got from dealers around here so they all seem to be inflated, but inflated equally. Like your etec my Mercury doesn't require me to replace the water pump, plugs, etc but while I'm paying the labor to pull the lower unit and check it I might as well have it done. Notice the cost for 300 hours on the etc is right at round $1250 in oil and the 300 hour service. The Mercury comes in at $1206 and is basically right on par with the Etec's cost of ownership.
We did our homework before buying and had quotes from all 5 dealers we considered at the boat show this past February before ordering and that not only included the cost of the boat but what their rates would be for the first 300 hours which for us will be roughly a year and a half of ownership. Granted, they couldn't get the oil right on the button but they have a pretty good idea of how much you will need and their quotes mirrored the below article as there was very little difference in the cost of maintenance to the Etec and Mercury 150's.
Again, not bashing the etecs, I'm just sick and tired of all the fan boys out there saying they are the best thing since sliced bread. There are pros and cons to each. As I stated, the tests on our boat with an etec had it running a few mph faster with a little better cruise economy, but when we considered everything the motors were fairly even from a performance/ownership standpoint. The biggest tiebreaker was honestly the noise, particularly at low rpm, so we would have went with the four stroke even if you through the questions out about the longevity of the motors. Both etec dealers did seem to be optimistic the G2's have corrected some of the issues they have had with the etec motors much like the etec improved on the ficht motors.
http://www.boatingmag.com/gear/boatinglab-tests-outboard-ownership-costs