Out of curiosity, do you have this same problem with, say, burning hands and a swarm of spiders? If so, okay. If not, why do you think that is?
That's a good question. No, I don't.
Thinking about it, mobs annoy the dramatist in me and they strike me as unfair. Squishing bugs/rats/bats is sufficiently non-heroic that I can just let the board game player in me say that these are the rules we play with. Plus, my inner dramatist can imagine the swarm retreating from what's an instantaneous effect, losing some of its number, but reforming in the square. Or the wizard didn't get them all. And so forth. Not to mention that it usually only takes one or two of those to take out a spider swarm. Genre-wise, I lump them into horror, where "it just keeps coming" is part of the terror.
But with mobs... they're so dramatic that it seems like SUCH a missed opportunity when the DMGII let clunky, imbalanced grapple rules mess them up. Bug swarms don't use %&&*% grapple, which takes so much time and looking things up in books. So that annoys the dramatist in me. The gamist in me feels like the DM's letting me win when the monster uses hugely suboptimal tactics. It's like killing an evil necromancer who only uses magic missile rather than his fifth level spells. So neither part of me is satisfied with them.
And then there's the fairness issue. By the time a party is facing a mob, they're at the level where the fighter inherently lags behind the glory hogs (CoDzilla and wizards). I find it unfair to players of fighters that take feats specifically to deal with large numbers of weak creatures if they get them ruled out of existence simply because the DM calls them by a different name. As a player, I'd want to know before going down those feat paths that the DM was going to make them useless just when they'd be most useful and dramatic and interesting.
The idea of a monster that takes something ordinary and makes it both a tactical challenge and a dramatic moment and does it without rolling dozens of d20s is SUCH a great idea. But I want it to be fair to the players. I want it play as fast and dramatic as possible. And I want to make the suspension of disbelief as light as possible.
When I use mobs as a DM, and I will, I'm going to have fighters with Cleave do double damage. Those with Great Cleave and Whirlwind attack might get triple and quadruple damage respectively, but have to move into the swarm to get them. I won't allow the mob to grapple, but perhaps replace it with a Fort save or dazed for one round (modeled on the distraction ability of swarms). And I'll just live with the suspension of disbelief on spells affecting mobs.