Out of 48 plants, only two are actually listed as female. (Some have no gender listed. Many, many plants are explicitly male.) And one of those two female plants is the useless Marigold. (It generates coins. It does nothing in terms of the main gameplay.) Fanon suggests that the sunflowers are female (and even draws porn of them) but the game doesn't say.
Out of 26 zombies, none are female. Not all are explicitly listed as 'he', but many are, and the others give the distinct impression of being male.
Peggle Nights somewhat sheepishly added a female character, since the original apparently had none. Rather than simply make one of them a girl (It's not like we could have told any different, probably) they made one with Lips! and Eyes! to set her apart from the others. Peggle also suffers from the problem of pre-filled high score lists, filled almost entirely with male names. (Although at least they don't *intentionally* put girls at the bottom of the pile. A female name shows up in rotation now and then.)
Out of games originally developed by PopCap, do any of them focus around a female character?
I am not in the slightest suggesting that PopCap hates women or anything like that. Just that it seems like, without some strong external force prodding at them, they tend to forget they exist... 'Default', here, will always be 'male'.