Regading routine maintenance, its expensive, and spare parts of Wagon R are costlier than EFI Cultus.
Wagon R zyaada ka'am nikalti hai, aur baar baar nikalti hai, due to slightly compromised build quality, I believe.
Wagon R has a relatively newer engine than EFI Cultus; K10B.
I believe, the newer an engine is; the better and refined it is. 