The first three (or two) gyms already put Venap users at a severe disadvantage. Choosing Venap is basically like choosing hard mode, one more disadvantageous gym won't do much. Also, any smart trainer would pick up at least one or two more party members, so don't be so hung over on gym types just because of the starters.

More cities? Really? Discounting Olivine, Cianwood, and (soon-to-be-renamed) Champion's Tower, There are a total of 20 cities, 11 in Caldera and 9 in Kirant, more than enough for 6 gyms each. Add to that the various Rocket/Orion subquests, backtracking, and overly long routes, your concern should be the absence of gyms. I also don't want Rocket or Orion having their own gym (I'm writing up a new background for Christina), we can have a Dark-type gym but I doubt we'll be able to put forward the "dark is not evil" message (which it actually is; the Japanese word used for Dark-type literally means "evil").