For one thing, the Phantom Fungus seems to have fallen out of the worst 50s B-Movie ever made--this can be fun, but it doesn't quite lend itself to the broadest range of games.
As others have remarked, the fact that it seems to be filling a space in a grid also detracts from its appeal. Who needs a monster designed by Linnaeus?
Just for the heck of it: Daemons have always bugged me for this reason, both in their role (filling the Neutral Evil Outsider slot) and their name (finding a monster for the archaic spelling of 'demon').
So, yeah, obvious contrivances start with a mark against them, but, as you've mentioned, some of them have attained to popularity. I think that the succesful metas have responded to situations of setting, rather than rules abstractions. A rust monster could have been invented by any writer working within a context that includes metal-equipped characters; a creature meant to serve as an instructive tool in a game of progressively more difficult tactical challenges cleaves too close to the gears--it has difficulty serving any other purpose.
But what about this plant business?
I'll admit that the task of getting a plant monster right doesn't come easy, but I don't think that's the reason for the phantom fungus's unattractiveness: this rose, by any other name (or type), still stinks. It's a bundle of qualities, not a creature; no new moniker will change that.
Plus, plants rule!