It would probably look better and sound more reasonable (realistic), if you could place most districts just around the city center (the first circle, 6 hexes). Some specific districts would still be possible to place anywhere, because those would look more realistic further away (airport, encampment, spaceport, harbor).
Or another idea - you can place a district only adjacent to another district, so the overall city could have various shapes, but still would be one connected "mass".
Sure, this would require a new balancing (of adjacency bonuses) and removal of a lot of limitations.
But in general, I don't really dislike the system as it is now, so I don't really call for the changes I proposed in this post. What I would hovewer welcome is removal of a lot of wonder limitations (especially when it's a combination of "next to a specific district" AND "next to some map feature") and probably also a little tweaking of the district adjacency bonuses, because now it really requires a lot of (too much of) thinking and planning.