You have 2 choices to make, if you plan to sell in thenear future, do NOT repower, you will never get the value back on them on a used boat, you will get more then the old power but no where near your repower price, typically from what I've seen guys who repower then sell take a big hit. If you plan to repower, plan to keep the boat for atleast 5-10 years, 5 is on the light side though, personally for me it would be 7-10. If your unsure of this time frame, buy newer for sure, it is a better investment for your money, that is the first choice.
As far as engines, I agree with much that you have stated, E-Tec's I've heard mixed things about, know 3 guys with issues with plugs fouling and engines going into winterization mode heading in from the canyon at 4000rpm...scary to me!! Also the 4 stroke technology is great and the way to go for value down the road.
Yamaha is very reliable but often heavier and will not have the punch of the line, but they are good on gas over all and quiet and to most are the best fit for a Grady since that was what they were designed to run and what most owners seek.
Merc Verado's are a good engine when running, and good on fuel, but not as good as they claim in some adds, but they are faster for sure for the hp. They love to run at higher rpms sop if you can utilize that that might be a plus. Personally I know too many guys who hate their verados so it would take a lot to convince me to buy one, but those were mostly the first gen first or second release of them where they had lots of issues, since then reliability has gotten much better, seems like a pattern with merc...issues with all new engines but then they become tanks after 2 years when issues are worked out, just like the optimax, they started out with tons of issues but then became a true workhorse and very reliable.
As far as suzukis, they are surprisingly good on fuel for the hp and often then not are better on fuel then the Yamaha's, but not quiet as good as a verado, maybe in between. They will have similar power to the Yamaha but not the power of the Verado. The new suzuki 4 strokes are very reliable as well, most on this site who repowered with them have nothing but good things to say about them, and most would highly recommend them.
As stated before, local dealers are important, are they reliable and do you trust them to service you engines, that may play a big part for service, for me it would since not all engine dealers are local to me by water, traveling by trailer is not reasonable nor sensible for me suince I do not trailer and would require permits to do so.
Get a price quote from all manufacturer's even if you plan to eliminate them, it might give you leverage with another brand to get a slightly better deal or some freebies thrown in.
Also, going to a new brand might require not only new guages, but new steering as well. Yamaha and Merc engines are NOT mounted on the same mounting spacing so that is an issue as well, so not having to modify your transom is a big issue. If you ignore that you might have issues where you will be playing with mounting heights and props fopr a while to tune it in right, and each manufacturer's shaft length is NOT the same, something else to consider if you change brands. Yamaha does have new fly by wire for their engines just like merc does, both systems are awesome but will add to the cost as well.
Best of luck, let us know what you choose!!