Both have pros and cons.
Pros: Better looking shape (even if old), more comfortable, more spacious, good resale, good and cheap parts availability, cheaper and easier maintenance, works excellent on CNG.
Cons: Older technology, no immobilizer, no power windows (but you can get after market).
Pros: technologically more advanced (engine) , standard power windows, better fuel economy (on petrol)
Cons: Smaller in size (less legroom), less comfortable, ugly looking (for most people but thats personal taste), more expensive spares.
WagonR: If you do not have rear passengers (or only kids), drive less and on good roads, and use petrol as a primary fuel.
Cultus: If you have adult rear seat passengers, drive more and long on bumpy roads, are concerned about maintenance and resale, and plan to use CNG.
Also there is a personal choice factor. I do not like small cars.