As far as I am concerned, yes. Most games I care to play these days have some sort of class, archetype, or similar structure. I find that freeform design games are more difficult to manage and result in groups with many characters that are too fuzzy a focus or over-specialized.
One thing I think is important about classes that many designers miss is that classes help define what the game is about. The characters' abilities define how they deal with problems and what sorts of problems they deal with.
An earlier post about siloing is also something to pay attention to. Often I find players gjo for "sexy" abilities and skip over useful and conceptually appropriate ones. Putting these abilities in a class or structure helps both the concept and viability of resulting characters.
When I was first working on my Nexus D20 system I was thinking in terms of Classes such as in T20 Traveller and Spycraft 2.0. I was mixing it with my idea of having Feats under Skills. I had more and more Classes and they were less and less different from each other. After a while I realized that I could make Classes all day long but there wasn't much point to it because it was just proving that the game system didn't need them in the first place.
A few things.
First, just because you can make classes doesn't mean the gm or players are as good at it or want to.
I would also wonder if such classes are broad enough. One thing that vexed me in 3.5 was all the classes that could have been handled by a slightly broader class with a few more player selectable features. Indeed, I wonder, since you mention spycraft 2.0, how many classes could have been done with soldiers + origin and feat choices? It sounds like you may be commiting the gm and players to a bigger design chore than warranted.
Indeed, one criticism I hear from former gurps players about that game is that they initially thought the freeform nature would be a boon, only to discover they were designing archetypal characters anyways.
Basically I think that level based games are starting to shed their need for classes. They have been together for so long that most people don't see how that could be but we have Mutants and Masterminds and D20 Call of Cthulhu already that don't have classes and they work fine without them.
I dunno. My opinion and experience differs here. I consider the skill system of d20 coc superior to brp coc, but consider its chargen markedly inferior.
As for M&M, I know many people who would like to gm it, but consider making villains a chore. Or fall back on the archtypes. Further, I consider supers to have somewhat different requirements, powers being a more important defining characteristic than skillsets in many cases.