The factory configuration decisions are the subject of a great deal of discussion in the community, There are a few other holy wars that RV builders fight endlessly. Most notable among them are a) what and how to prime the metal parts, and b) what kind of engine to use (automotive conversion or Lycoming). There are plenty of places online to see a raging discussion of these topics. Since this is my Web site, I'll write what I think:
I'm tending towards the minimalist end of the spectrum, but there will be non-zero amounts of primer on my airplane. I'm building a QuickBuild, which is primed at the factory with a product which, according to its manufacturer "offers no significant corrosion protection." It's not practical to reprime with a more protective primer, let alone etch and alodyne, parts that are already assembled. So the parts that arrived preassembled are going to remain unprimed (by me), except for purposes of painting. I'll still prime surfaces that are going to be pained, such as the visible portions of the interior, for purpose of paint adhesion. I didn't prime every square inch of the empennage, though. After all, if the bulk of the airplane (wings, fuselage) aren't primed, what good does it do to prime the empennage? What I am doing is priming the regions that I think are most susceptible to corrosion. That's the contact surfaces. For one thing, moisture can get trapped in between parts. For another, there will always be slight scratches in assembly. Those scratches often penetrate the alclad layer, allowing the part to corrode. So where the ribs meet the skins, I primed the skins. The ribs I primed in their entirety since they're small and easy...not much weight or labor penalty. But the bulk of the skins are not primed. I used rattle cans of Sherwin-Williams GPB-988, a grey self-etching primer. Occasionally, I use zinc oxide, because I had some lying around. Plus, real airplanes are made of aluminum, and real aluminum is green. So I had to have a few green parts. That stuff doesn't adhere well without etching the surface. Etching adds labor. It means either scratching it lightly with a Scotchbrite pad, or scrubbing the parts in Alumiprep. If it weren't for that, I'd have used it more.
So if you look at my fuselage, you'll see parts that are grey or green, surrounded by a lot of factory-primed parts that are dark silver, the color of the primer that Van's uses. It looks weird, but the visible parts will probably be painted or upholstered or covered with seat cushions. I could've bought the same primer they use to avoid this. However, if I am going to prime, it makes little sense to use a product that offers no corrosion protection.
The factory recommends a normally-aspirated four cylinder Lycoming aircraft engine between 160 and 200 HP. Period. There are a few specific models of the O-320 and O-360 families that Van's supports, but with enough sweat you can make many member of those families work. People have put in turbocharged Lycomings and the beautiful Walter inline engines, but Van's recommends you stick with their choices. The other popular choice is an automotive conversion. People use Subarus a lot, and a few use Mazda rotary engines. A handful use a V-6. These intrigue me, and I looked into the Subaru conversions quite a bit. I am on my third Subaru car, and I'm fond of them. The engines are rugged, rev happily and with their short, stiff crankshafts, have high resonant frequencies (i.e. probably won't interact with a prop's modes.)
Yet, I'm sticking with a Lycoming. Haven't decided which one yet, but it'll be fairly "normal," with the exception of electronic ignition. With avgas at $4/gallon, saving ~1 gph with electronic ignition makes sense. What I've learned about the Subaru conversions scared me away. I'm not worried about the core engine itself...it's well designed, by people who I trust know what they're doing. What worries me is all the claptrap that surround the engine that has to be modifed for aircraft use: prop reduction drive, the prop itself, cooling system, fuel system, engine control unit, etc. There are some nasty kludges for sale. And they're no cheaper than a Lycoming. I'm looking at $30K forward of the firewall for any new engine and prop. That's another advantage of the Lycomings: there are overhauled or used engines available. They're not as easy to find as they used to be, but they're out there. Why are they hard to find? Lots of people are building homebuilts!
Most conversions don't allow you to use a normal hydraulic Hartzell constant-speed prop. You have to use an electric prop. That, to me, is another disadvantage. I am willing to concede that Subaru engines are more evolved and refined than Lycomings...but Hartzell is pretty good at making props. MT, who makes an electric prop you can use with automotive conversions, are pretty good too, but they're ~2x as expensive as a Hartzell.
While we're on the subject (I'm on a roll now!) of how "ancient" and "obsolete" Lycomings are, let's explore why people say that. Why have automotive engines evolved so much? Because they had to, and because they could. Emmission and fuel economy drive auto engine design. By "fuel economy," I mean part-throttle low-power cruising fuel economy that you see in the window sticker. Auto manufacturers went to computer-driven fuel injection and electronic ignition because it let them make their engines economical and clean burning at low power, yet still burst occasionally to high power without stumbling, missing, etc. That was hard to do with carburators and mechanical ignition timing. The hunks of metal sucking, squeezing, banging, and blowing have not evolved significantly. Yes, liquid cooling has its advantages, but I care about weight, reliability, and fuel efficiency...are auto engines that much better in any of these categories?
Airplane engines live a different life than car engines. They spend their lives at 65% power or higher. They do not undergo rapid throttle changes. They spend hours and hours cruising at one altitude, at one speed. When either changes, it changes slowly, and the pilot tweaks a knob or two to keep things running happily. I don't understand the allure of FADEC, single-lever power control, etc. In a three hour flight, how many times do you mess with the engine controls? I am VERY interested in having my airplane engine start as easily as my car engine, but that's a poor reason for sticking in a bunch of sensors, electronics, and software in the loop. One electronic ignition should work wonders there.