Hi Paul,
I have been in your shoes twice now. I am just wrapping up another certified revamp...
I would really rather have an experimental, the problem is both times I had too much of a certified cub to waste it by selling off the paperwork. A complete cub can bring you a lot more $$$ than paper, if you build it back up yourself. Then you can do an experimental "right" if that's where your heart lies.
IMHO, a molested cub with a few tweaks here and there is not an experimental worth the value hit. There are some really sweet cubs out there that are certified. If you are going to go experimental you may as well go with a nicer than cert. motor(ie: o-340, o-375), better flaps, better ailerons, longer wings (or shorter if that floats your boat), and an extensively mod.d fuse... Wayne Mackeys cub is a great example, but at least I'd build on par with one of the more tricked out Smith cubs.
A couple thoughts I had:
The commercial argument is bogus, plain and simple.... If you are not holding a 135 cert. there are very few ways to make money with your cub, and a few of those ways you can do without a standard airworthiness...
Do you have a 135 or plan on it? Coincidentally, most cubs I have seen (Standard A/W or not) would have a tough time passing the muster on a 135 cert...
The value question is too broad to apply to the a/w certs...I can't think of a better example than a nicely built RV-6. It will almost always bring more $$$ than a mediocre certified plane of similar type... A smith may not bring as much as a new CC Ranger, but I'm guessing you won't have as much in your rebuild as a new CC ranger costs either...
Saving money through owner maintenance is almost as bogus. A properly maintained cub should have an annual that takes less than a half a day... Owner assist that and your annual will probably not be over $400... mine has never been... Heavy maintenance (the kind most guys will send out regardless of a/w cert) should be pretty far in the future on a bird that just got built. But having said that will you replace jugs or tear down the engine on your experimental? If you will send these out to your mechanic, then again the savings is not what it's played out to be...
Just opinions of course
Take care, Rob