DaremihC don't worry too much, your riddle wasn't that bad. I kept circling round a materia that was in a Mako reactor, and kept thinking of Ultima, but that seemed like you'd have mentioned the well instead. I don't quite get the extra clue though...

My guess for the new riddle is Wutai side quests...

Twelve ways to see, twelve ways to go. (No idea)
Take one there that comes with Throw. (Yuffie has to come with you)
She'll meet her fate, or will she not? (The scene on the mountain)
It's time to take back your spot. (Spot I guess being a reference to materia)

The watery one will be your treat (Leviathan)
If you manage to defeat. (The pagoda)

EDIT: If thats right someone else take the next riddle.