first of all OP has asked the choice between two cars he finalized, it is his first car and he wants a brand new one with minimal issues so suggestions might be welcome but the thread has turned into a war of personal bias.
ABS is a very important feature no doubt but it can't counter stupidity, most imported jdms have more accidental damage compared to PKDMS that too in a country with better rules and regulations implementation and execution than ours. At my home there are 2 cars without ABS (more than 15 years old) and 3 with ABS(2013 and above) models, and driven sensibly one can make out of emergency situations just as well with and without one, understanding change in grip is what matters, even ABS cars can skid when turned to hard.
2nd Braking hard with or without ABS at 150+ destabilizes any car (except premium models that are designed to be driven at high speeds such as German sedans).
in all situations, wagon r delivers better power than vitz. as somebody stated physics, wagon r has 200kg weight advantage over vitz with same hp and better torque delivery being a manual so a vitz with driver only weighs as much as a wagon r with four persons.
16 valves vs 12 valves, wagon r has 3 cylinders and vitz has 4 so both cars have 4 valves per cylinder and that is for 1sz vitz only that isn't as common as 1kr fe which is 3 cylinder and 12 valves.
manual over cvt for towing
and did anyone look into how much knocking vitz 1.0 does with a/c when trying to keep up with traffic
wagon r does have body roll, but it is exaggerated by its haters. have yet to see a rolled over wagon r news on pakwheels yet, I posted a pic where I'd to push 9th gen to 5.5k rpm to keep up and overtake a wagon r going beyond 140 and it certainly didn't look unstable.