Why is most aircraft livery painted, rather than vinyled?
Changing the status quo always takes time. Aircraft have been painted almost since the dawn of flight (and the very earliest aircraft were still doped to stretch the fabric over the skeleton). That is reason in itself for antique and historical aircraft and their replicas to be painted instead of vinyled.

In addition, most liveries come factory-installed right alongside the host of other options available. Most high-end private jets as well as the big commercial ones are built-to-order inside and out, including the customer's brand livery. That livery, much like the factory color of a car, often stays with the plane its entire life, with only routine touch-ups performed as a normal part of maintenance. Refitting a fleet with new livery and/or interiors, until very recently, wasn't done often; Southwest's "Canyon Blue" livery change was noteworthy, as was AA's fleet rebadging, and neither airline bothered repainting planes that are on the way out anyway; the aging Super 80s as well as the 757s and some 767s are still in classic AA silver livery and will be that way until they're retired from the fleet.

So, aftermarket vinyl livery's market share is already somewhat limited; people buying a new jet will get their livery applied at the factory, and people buying a used jet and wanting the livery changed significantly are in for quite an expense even if they choose vinyl; the old painted livery will usually have to be removed and the plane refinished in a new base coat before the new vinyl decals are applied.

I would also venture, having seen aftermarket vinyl applied to other vehicles, that even if the utmost care is taken in applying it, the decal is always going to look like a decal, and it may not age well even with a meticulously-maintained airframe. If you're paying \$65 million (base price) for a G650, \$25,000 (or even \$100,000) for custom livery is a drop in the bucket. 

Now, your 172 or Piper Cherokee sport pilot might be very interested in personalizing his plane on this kind of budget, as would an aircraft club of part-owners, or your self-employed commercial pilot like a crop duster or charter bush pilot. Vinyl on small planes thus makes more sense; however, it's still a significant expense, and a purely cosmetic one, so it's still rare to see a plane's factory paint scheme change significantly aftermarket, except for niche uses like aerobatics and stunt flying.