Actually the way that the Cruise is configured, it would be easy to accommodate both comedians and dreamers. After a given number of comedy boats, insert a "National Geographic" one, and/or possibly also a "silent" one. Split the queue into these two or three lines, and adjust the mix of boats depending upon queue popularity. There is enough distance between boats so that the noise of a comedy boat wouldn't disturb a NG/silent boat; at the Falls the noise of the water overwhelms any two passing boats.
Methinks that a completely silent boat option would be particularly exotic at dusk and after dark.
Indeed there are all sorts of ways to vary the JC experience. For instance, we are all familiar with "murder mystery" dinners, boat/train excursions, and the like, wherein a few period-costumed actors stage a "murder" for the audience to solve. While a "murder" is probably not appropriate to Disneyland, some other mock-challenges could be presented - for example the last-minute "stealing of a boat for a getaway" with hapless Guests trapped on board, followed by "the law" in the next boat. [Distant echoes of Disney's The Great Locomotive Chase.]
With the addition of a few exotic lights and sounds in the jungle, you could have a boat skippered by Mulder & Scully types, telling passengers they're looking for a reported UFO landing and asking for everyone to be alert accordingly.
If Disney can license Indiana Jones & Star Wars from LucasFilm, they can probably get Universal to allow the Creature from the Black Lagoon to clamber stealthily onto the rear of a boat at night, lumber past terrified Guests to the [beautiful damsel] skipper and carry her screaming over the side, leaving the Guests alone to worry about getting the boat back to civilization. [An "undercover Guest" CM would "figure out" how to operate the boat.]
The famous jungle cruise along the Nung from Apocalypse Now also comes to mind, but I can't think of any part of that which wouldn't be too hairy for Disneyland.
Speaking of Indy, I rather like the idea of adding a "cave tunnel" segment to the Cruise route to take it through a bit of the Temple of Mara. Imagine a troop carrier careening towards a suddenly-appearing Cruise boat, near-missing it at the last moment.