I was exactly in the sane situation couple of months back. BRV outsets altis in all areas, but resale. I still went for BRV as being salaried person i won't be changing my car in next 5 years. I am actually glad with the kind of response BRV has got. It means that although resale wont be like altis, but wont be a disaster like avanza etc.
Now i am driving BRV-S for 1.5 weeks now and so far totally satisfied. I didnt required a 6 seater as must (as we r 4 adults and 2 toddlers in house) n however it comes really handy. Apart from ground clearance, overall height and options you get makes it a totally worthwhile ride. Haven't heard of and faced any problems with pickup etc.
In a nut shell, only thing you may want to consider is resale if you are comparing with altis.....
Hooe it helps.