Many people keep their money and resort cards on a neck "pouch" that is waterproof. They sell them at most resort gift shops now and also at the water parks. (You can see a similar one
HERE.)
I didn't find the lines for lockers/towels to be that long...
You won't be able to wear flip flops on the water rides, but you can wear water shoes or "aqua socks" like
THESE. (At least you could the last time I went to Typhoon Lagoon.)
This is what we did -- went to MGM until we were sweltering and then headed to TL. We didn't have as much time in the water park as we might've liked, but we had a blast and felt very refreshed.
Hope that helps a bit.
Eileen