Sometimes it seems like the boats run late. You may wait a while (10-15 minutes), but it is a very nice ride once you're on the boat. Also, WL shares boats with FW, so depending on which way the boats are running, it may add a few more minutes if you stop at FW. Also, there's always the option if you just miss the MK boat to take the CR boat then walk to MK from there.
We love WL. Don't let the transportation issues concern you. Every resort has transportation issues. Also, at the end of the night if you stay for fireworks either get right to the dock ASAP or take your sweet time to let the crowd thin. We never waited more than two boats. Remember, the only resort that will give you a guaranteed "no wait" return from MK after fireworks is the CR because you can walk.