FAQ: Why bother with a class system, when it essentially is emulating a skill system?
Bradd W. Szonye
(This FAQ specifically addresses an objection to d20 Modern, but it also addresses the larger question of "why bother with a class system at all?" — ed.)
Because it encourages players to actually think about their characters' core concepts and themes and then stick to them, rather than munching out a bunch of arbitrary abilities that sound cool. It also encourages players to make well-rounded characters rather than over-specialized monstrosities, because the level system keeps abilities within a reasonable range of each other. Without those two elements, it's very easy to run into overshadowing and niche invasion problems.
It's not quite as good as a setting-specific class list like D&D has, where you can represent an entire concept with just a few notes (ability scores, class, and level). Good classes like that are a kind of shorthand that helps reduce complexity and bookkeeping. Don't think of classes as a straightjacket that limit your flexibility; a good class system also leaves many things unspecified so that you can fill in the details with roleplaying. (I think point-based systems tend to overspecify characters from the role-playing angle in a misguided attempt to formalize character details that are better encoded freeform on a sheet of looseleaf paper.)
However, a D&D-style class list also ties you to a specific kind of setting, so there's a trade-off between detail and flexibility. Gamma World, d20 Modern, and other setting-specific Modern supplements should help with that; you can think of the d20M basic classes as placeholders, if you like.
So many complaints about class & level systems just don't seem to recognize the benefits that classes and levels give you. By imposing certain mechanical restrictions — NOT role-playing restrictions — they make it easier for PCs to coexist without stomping on each other, and they make it much easier to get into the game, whether you're a new player or a GM who needs to prep a bunch of NPCs.