Haven eaten at both the Blue Bayou and Rainforest Cafe on the same trip, I would prefer to return to the Rainforest Cafe. I have only eaten at the BB twice, both last year, Rainforest Cafe several times. I often crave BB's Monte Cristo sandwich, but I didn't think the restaurant was all that it's hyped up to be. Each person will basically pay about $25 - $30 at the BB if you go during dinner.
Rainforest is cheaper (but still on the pricey side), you can get a burger for about $8.00, fries and drink are additional, and yes you do get more for your money. Also offer an AP discount for those of you AP holders reading, we kept forgetting to use ours throughout Downtown Disney!
Think I read you're going with a teen? Rainforest will be more interesting and fun. Oh, and if the line or wait is ridiculously long, you can always ask to sit in the bar area - I believe those under 21 can't sit at the actual bar, but they have small tables in that area which are open to all ages. You should be seated almost right away. But you'll miss out on all the fun animal stuff, doing this is better if you're a party of 3 who are only interested in eating and not really there to see the rest of the place.