Yes, it goes against what you would think the normal line of technology would be, simple to complex; unsophisticated to sophisticated. However, that's a false impression , here. In some ways the flintlock is as complex a technology as the wheellock.
Available evidence suggests that wheellocks were developed first. It's somewhat debatable as to precisely when- there's one surviving self-igniting gun called the Monk's Gun, in Dresden, that's been variously dated 1460 to 1520 and that muddles things. But perhaps you could date the advent of the wheellock to when they worked well enough for people began to worry about them. Because the matchlock system required a lit match to be burning on the side of the gun, it was not concealable ( imagine carrying a smoldering cord inside your pocket). A wheellock was concealable, and so with the advent of the wheellock there's the advent of the pistol ( again, the Monk's Gun might be the first pistol, if it was really from 1460) In 1517 the Emperor Maximilliam banned self-igniting guns throughout the Empire, so we can assume that the things worked well enough, were common enough by that date to attract notice . Da Vinci was drawing the mechanism by around this time, too, and putting it alongside a drawing of a similar fire starter in the Codice Atlantico. There's a real possibility, indeed, that the wheellock was actually mostly pre-existing technology, that there were little spring-driven fire starters around, and that some bright gunsmith just stuck one onto the side of a gun....(and again, the Monk's Gun has a similar, though not spring driven, mechanism that might have been a fire starter).
The flintlock arrived sometime in Germany around 1530, perhaps because Charles V encouraged firearms development and got rid of Maximillian's prohibition of self-igniting firearms. It probably was developed as a result of the spring-actuated matchlock: the first matchlocks had a simple lever holding the match- pull the lever, the match went down into the pan to ignite the powder. After 1500 or so, there was a spring catch, a real trigger, that could simply be touched to set the spring-driven serpentine into the pan to set off the gun. Soon after, someone would wonder if they could make a serpentine hold a flint and wallop a piece of steel.
These early flintlocks, called snaphaunces, required something new, however. There were two ways of striking a spark for starting a fire in this period. You could take a chunk of flint in one hand, and strike a steel loop against it to make sparks, or you could strike a piece of steel or even flint against a piece of iron pyrite, or marcasite. Marcasite is iron sulphite, and sparks pretty readily. That serrated wheel on the wheellock ( and the serrated bar on the Monk's Gun) seems to have been the normal way to make iron pyrite make sparks ( similar to the way cigarette lighters work now, though the don't use marcasite). The marcasite doesn't have to be any precise shape. With a flintlock, though, the flint is driven against the frizzen ( or steel) and sparks are knocked off that. That means you need a small piece of sharp flint, shaped so the cock ( or hammer) could clamp onto it. So, first, they needed flint knappers to learn how to make gunflints. They also needed to develop the right kind of geometry for all that to work- the flint is raking down across the frizzen, levering the frizzen out of the way, which pushes aside a cover over the pan, exposing the powder. That's not simple- there are two radii and one curved surface to get right for it to happen well, as well as a good stout mainspring ( even today, hunters who use period reproduction muzzle-loaders will tell you that a cheap percussion lock will work, but not a cheap flintlock). It is quite possible ( even probable) that the reason wheellocks were used well into the 17th c. was that getting this new flintlock system to work well enough to be very reliable was hard, that wheellocks were generally more reliable than flintlocks. And reliability is a very important thing for a firearm, whether it's being used in war or for hunting.
So, TL:DR, though they had fewer parts, flintlocks were as complex, and a newer technology.
Torsten Lenk: The Flintlock, Its Origin and Development