It's worth mentioning that all cluster attempts will diminish from the number of possible villages. If you want to maximize villages, clusters are rare. Do you guys build villages only on your roads? Because they have some pretty nice yields by themselves. I'm no expert (only King difficulty), so maybe that

and subsequent specialists are more valuable to you then the raw yields, but just commenting from my knowledge of mechanics and synergies:
-Villages are better for Rationalism
-Farms are better for Imperialism and Cathedrals
-Villages are better for Cultural victory (?) at least after hotels
The guide would have been nice with tips for including villages.
Ideally, I've been trying to pattern villages around 3-farm triangles, something like:
(O is empty, U is village, X is farm)
oUoXoUo
OoXoXoO
oUoOoUo
This layout is nice, because if you replace the southern-most O (empty) with a farm, you can make another triangle to the south of it and repeat the pattern. This farm you've added will get +2

, benefiting from the bases of both triangles. The other O's can be used for GP improvements, and this is all, obviously, land permitting.
oUoXoUo
OoXoXoO
oUoXoUo
OoXoXoO
Also,
When was this made possible!? I had believed bonus tiles, in Civ5, could only be improved with their respective improvement. Have I been playing the mod all this time without noticing VP fixed that? Or is it another mod your using?