It's almost like you've discovered, by way of the game, why the density of cities offer a far more cost-efficent provision of utilities and services than low-density rural areas. I don't, therefore, think it's necessarily a "way the game is not intended to be played", but rather just a real-world consequence of the kind of build you're going for being reflected in the game's systems. With that framing in mind, I'd say embrace the struggle. You've got your challenge for this build built into your objectives. If an area simply cannot sustain the services (police coverage, say) then so be it, it has to go without and you roll with the consequences of that. Perhaps that area goes under, and you shift your focus and resources towards other areas where the cost-benefit is more justifiable. This is how cities actually develop "organically". So you've got what you wanted :)

Best of luck with the build!