Yeah the Marlboros and Tonberry's are a pain in the ass. Especially the Mega Huge Tonberrys in X-2 in Via Infinito (or you can just CatNip and Trigger Happy their ass xP).

However, the most ANNOYING enemy i find, is the Gigantaur (Giant Cactuar) in XIII. The 10,000 needles pissed me off for days, until I realised it can be fogged (or pained) to stop attacking temporarily.