Unless you have concerns about her raw combat values not stacking up, the Fungus Queen really doesn't need class levels to serve as a BBEG. She already has many of the advantages of the succubus and the vampire; impersonation, telepathy, teleportation and the creation of loyal spawn. Then of course there's the plant empathy, which is as versatile as your imagination.
I am of the opinion that careful selection of her minions would be enough to make her memorable, especially if you're advancing into her lair. The 24 HD limit of Create Spawn is enough to have a pet succubus (more energy drain and mind control), a dryad (entangle) and a full-fledged druid. Give the druid a companion and an awakened tree. Summon the succubus' babau. Add in a few strands of ivy trained to release dangerously unstable pieces of masonry on command, a flanking shrubbery or two, a lovesick assassin vine, a dominated bard and, just to round out the confusion, a dominated shambling mound.
That said, if you want her own combat prowess to matter, I'd go with Monk (Maneuver Master), probably focusing on bullrush or reposition to drive people into bad spots. The Lunge feat would supplement nicely if you feel she should threaten through the sporepods. You could of course take advantage of her high charisma and go with bard, making her cannon fodder significantly more dangerous and adding fascinate to her repertoire.
