Being Maruti is the difference

One should prefer WagonR to Santro, as WagonR gives better mileage, is more spacious & airy inside - tall car (total space inside) & gives a more comfortable feeling.  Maintainence is low (like all maruti cars).

Santro is much smoother than wagon r but maintenance wise wagon r is cheaper than santro

The difference is Hyundai is korean while Suzuki is JAPANESE.. This is all that I have to say :-)

Santoro: Good built, equally good performance & economy as the Wagon R. Service can get expensive especially in cases where you need to replace Oil Sumps, Master brake cylinders etc

 

WagonR: Very well built, Great performance and economy, head room & ride height. Very easily maintained. Great prices at Maruti dealers for any spares, replacements, Service available at possibly the remotest of locations

If you can do with a slightly less quiet engine, get the WagonR. 

Wagan R is a popular & proven model in Japan, it also very comfortable in indian roads. Santro is expensive maintanance , but good comfort then WagonR.I allways prefer Japanese Cars then Korian.
G.Venkateshan..................... Coimbatore