The green trails are awesome at Alafia. Fast and flowy with great scenery. Some call them boring, but I'd say those people are peddling too slow. There really isn't a preferred direction either.
Personally, I hit my favorites first and then ride the greens last. My preferred route is North Creek (taking all three hard options), then cut through the shortest part of Riverloop on my way to Bridges via the jeep road. Take both hard options off of Bridges (Shelly's loop and the difficult end of Bridges). Next I'll hit all three Rabbit Ears, then Rollercoaster and Moonscape. Finally, I'll head over to Gator Back and then Rock Garden (it's two difficiult and one intermediate options) and Sand Pine last. Ask 5 people, you'll get five different answers.
Keep in mind that Moonscape and Gator Back are extremely technical (roots, climbs, drops) and clay based. They are completely unridable when wet. Seriously, if you hit the first climb and your tires are already full of mud, walk your bike out. Riding them wet will destroy the trail and won't be any fun anyways.