I like the idea of "rarity" for any of three purposes:
1) World-building. If you ever tried to randomly generate a nameless town (I ran an itinerant campaign) in late 3.5, the table in the DMG were worthless. To borrow from computer science, rarity provides an extensibility point.
2) Complexity/difficulty. I have no problem with the "fighters are for noobs, wizards are for vets" mentality from 1e -- though I like having sorcerer/warlock for noobs who like magic. Being able to immediately look at the complexity of a new class (PHB2, Dragon, whatever) would be helpful. I'd like them to rename it, though. And not make it a big deal. Hey, Hero System has pretty stop signs on problematic rules. Why not D&D?
3) Roleplaying, um, density. Assassins and paladins work poorly together. So did 1e barbarians and wizards. Having a marker for classes that have some baggage might be a good thing. Maybe the fighter is common because you always can use another meat shield, the re-renamed thief gets "uncommon" because stealing from the other PCs is somewhat rude, the paladin gets "rare" because of the 1e assumption of "evil-hating neutrals" or 4e antihero ideas can be a bit crimped by a holy knight-in-shining-armor for a conscience, and the assassin gets a "rare" because it takes a certain sort of group to be comfortable with wholesale murder for hire. Again, renaming and letting it be a footnote thing would be welcome.
There is no way to actually establish true rarity of a rules construct in a P&P RPG. I don't see any of the designers being dumb enough to try.