Ummm interesting question.
You are basically compering a sedan with a cross over. I have never kept a Civic but yes had an earlier model of Altis and for the past 4 years I have a Suzuki Grand Vitara the (previous generation, it has bigger body with a 2.0l engine).
Altis, drive was much smoother, Vitara is a little bumpy but that is how cross overs are - because they are made for a different terrain. In Norther Area, or in snowy/muddy areas you get extra confidence in a cross over as chances of being stuck in these conditions are much lesser than if you are in a FWD/RWD car.
Safety features: Vitara
Fuel wise I think the current model of Vitara are much better than 1.8 Civic/Grande... Guess the owners of Vitara can give you right information (mine is a little heavy as it is all time 4x4).
Parts availability, the routine maintenance parts Vitara are not a problem but others can be. But keep in mind the built quality is much better than our locally produced cars (sadly) so they last much longer.
Resale: Local built cars have much better resale than Vitara... but you will be buying Vitara at already depreciated price... so it wont hurt you too much in 2-3 years time. Please keep in mind, Vitara could take much longer to sell than a Civic or Grande.
Personal opinion: I like Vitara very much but I was turned off with the size of the current generation... it is a slightly bigger version of Swift...that is the very reason that I am still holding on to the previous generation... having said that, in case if I have to buy a vehicle in the budget of 3.5m, I still might go for Vitara.. umm maybe that is because I love to keep cars that slightly different than other cars on the roads of Pakistan 
