I've always seen the three water generation options (transposer, crucible, dirty water) to have different pros and cons, but to be about equal in the long run. Dirty Water method requires more steps and either more complicated automation or more personal time. The upside it is the cheapest in terms of leaves/saplings to use, and the fuel required to make it is a byproduct of getting leaves/saplings. The transposer requires power. The upside is you get some saplings back and it's super easy to use and you can use it the moment you get a battery and a water bottle (aka, from the start of the game, without crafting a damn thing). The crucible doesn't give back saplings, like the transposer, but also isn't cheap like Dirty Water. The upside is it doesn't really require any fuel at all, and is much easier to automate than the Dirty Water method. It's sort of a middle ground between Transposer and Dirty Water.
So yeah, I think they are all totally valid methods. In my current game, I am using Dirty Water exclusively (hooked up to a MFR tree farm, Liquicrafter, and Redstone Furnace to automate the whole process now). But I think in the next I'll go with the Transposer. It's fun to try new things!
EDIT:
Watering can speeds it up just fine. And if you're making a machine that needs books and you don't have sugar cane, you're doing something wrong.