It doesn't increase the resistance, if you find it easier to do it that way, that's fine.
As for the other question about 3 phase, it depends on the number of magnets you want to use and the power you need.
The 12/9 arrangement works out nice for the common size magnets to fit a disc about 11 or 12" dia. This for convenience can be a brake disc. The output suits an 8ft prop.
If you need more output, say for a 12ft prop, to keep efficiency up, you need more magnet material. As the speed is lower on bigger machines it makes more sense to increase the diameter and use more of the same magnets, hence 16/12 or 20/16.
Also to answer another point, your drawing is for a single phase machine, you only need one rectifier. It can not be connected 2 phase with the coil and magnet layout you have.