I've often wondered if changing the configuration of the boats into rows (similar to Pirates/Small world seating style) would be feasible/worth it. The bottle neck right now seems to be that only 2 people can load or unload into a boat at a time. Instead of 2 people moving you could probably get like 8 or 9 rows going at once.
Another idea I had to "fix" JC capacity would be do both Load and Unload at both locations. This would require that the boats be able to pass each other, and also a change to the queue
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Its always interesting to me that JC/Pan sells out so quickly on G+, when I don't think most people would actually put them in their top 2 favorite MK attractions, it's all just low capacity with 0 height restrictions.
Side note, just found your podcast last week and I've really enjoyed the past 2 episodes!