There definitely is a trend, but I wouldn't say it was strictly percentile driven. Games have evolved quite a bit from the days where rules could be referenced as 1.2.1.3 - Character Routine, but that is not to say that games have gotten less complex.
In my opinion, it is the gamer that has evolved. There is a part of me that remembers the queer little straight-jackets I would don to play a game. Mostly it was an unyielding drive to understand game systems. I would accept just about anything to be part of a game, whether it was D&D, GURPS, or Palladium. But I think those rules evolved in a very small ecosystem where being different was far more important than being playable.
Currently, maybe 10 years, we see a shift in game design, where rules are defined more by genre. The early days of RPG's were forever compared to their ability to reflect perceived realities in wargaming. Now it is more important that rules reflect the reality of the setting. Robin D Laws, for example, made a tremendous game out of Vance's Dying Earth using nothing more than a d6. A percentile system wouldn't add much more if such a game was converted and might actually weaken the mechanics which make DE such a unique experience.
The universal language of discussing probability is a very powerful tool, but it isn't the be all and end all of gaming mechanics. This is evident even in d20 games. It seems to me that a percentile system adds a greater amount of transparency to gaming than most abstract systems, but transparency is not necessarily the goal of every game.
Warhammer is an excellent example of a pervy baroque style of game. It has percentages, yes, but also contains a magic system that doesn't follow the core mechanics exactly.
One argument I made in the BRP playtest forum is that magic, by its very nature, should be pervy to the core mechanics of the game. This was a difficult argument to make, as it is counterintuitive to the strengths of a percentile based mechanic. Nevertheless, it is an argument I am still willing to make, as the definition of magic, IMO, should not be so mundanely described using the same context to describe common action.
Please pardon my drunk posting. My excuse is that I am more reflective in these moments.

While d100 systems consume most of my time, I remember with great affection the time I spent creating a game world/system based on Ultima II. A transparent, percentile based, mechanic was out of the question for me. It would still be, if I were to pick up that project again.
For me; again I apologize for the long rambling post; percentile based mechanics are best suited for game where the setting is more important than the rules which govern a characters interaction. Thoughtful games - that's what occurs to me, first and foremost. Games where the acquisition of power and the driving need of character development (powers, feats, abilities) is secondary to the interaction of players with the settings are more conducive to a simpler; and inclusive; percentile based mechanic.
Ok, I'm done. Did I even post to the right thread?
Yours in gaming,
Arthur