Yes Alto has very good road clearance as compare to Santro, Santro some times hit the road breakers if 5 persons travelling.. Alto having Good CNG millage on long route, Good AC but not as good as Santro have.. I have also used both but was very very disappointed by Alto engine, fuel consumption, noise in cabin, Seats were not comfortable..
My personal purchased and used first car was Santro plus that was real joy to drive.. Then Alto 2002, Then again santro 03 Exec version, Then Wagon-r 2001, then again Santro Club 2007, Then Mehran 2011, Now again Santro Club 2008 :). But have also used my bro, sis, and father cars, Civic 2007 Rebon / Ek Wagon / Baleno / VITZ (The BEST CAR) / 88 corolla / 2007 Diesel Corolla / 2013 GLI Corolla.
Over All Engine performance, Cabin Space, seating and build quality is very good by Santro.
Regarding the Pathakha problem is not a regular problem, its on CNG only in case if your CNG settings are not good or plug wire, coils are week, Just a maintenance issue.
Once this problem faced in my Exec 03 but it was solved very easily by replacing the coils and plug wires, Coil costs only 2800 from bilal ganj and new original plug cable costs 1475. And after that 1.5 Year passing no such problem faced, then got a clean Wagon-R so i change the car.