I think the towns without gyms certainly add something more to the game by just bringing Hoenn more alive.And with a lot of the towns being so unique - Pacifidlog being the obvious one, you don't find yourself just wanting to cycle right through them.
However, on the topic of Unova, as most people are comparing the two regions, I wouldn't say the lack of towns without gyms was a problem, or how you have long sequences of linear gameplay (e.g. after defeating Lenora) - if anything, I liked those bits as they made it more cinematic. I would say the biggest problem is more that the route layout is so linear - only Nimbasa and Opelucid have more than one path through them (in Black and White at least, I don't know about the sequels). By comparison, when you look at Hoenn, or Johto/Kanto in HeartGold, its all more inter-connected, with all roads in Hoenn leading to Mauville City for example. And Johto only has two towns without gyms, yet its fine.
So in answer to the question of whether or not there should be more or less gym-free towns, I would say I'm fairly indifferent, provided each towns has enough character, and preferably more than two ways in/out.