Well - For starters Vios is a sedan and IST is a hatch. Vios is Thailand / Indonesia built (like the Avanza) vs IST was Japanese made. Both cars are plenty used in SL , and both lines if i am not mistaken have been discontinued. Vios now goes at Ativa i think and am not sure which replaced IST.
Personal experience , i preferred the IST to the Vios despite the space handicap. But mind you IST was 1.3 ( there were a few 1.5s) whilst Vios is 1.5. I can remember the i.3 IST did better fuel vs the Vios, and creature comforts IST was much better. In fact in the West the IST was sold as one of the iconic "Scion" brand name dubbed "Urban cruiser". The last IST model was quite the looker for me. The last Vios model was based on the Yaris / Belta in fact , despite a few cosmetic changes it was hard to dis-certain one from the other. I think the Vios had more bling like a nickel shell and slighly modified headlights + better kit. But you dont get many examples in SL and i think many were imported for Airforce +Navy usage.
The experts must correct me but both cars had the 1NZ engine, although not sure about the gearbox for Vios.
Don't know about the latest Vios , but the one before which was very popular in SL wasnt very comfy for me and had noisy suspension. Dont know whether it was a build quality problem / the example which i used was maintained bad. On the contrary the IST faced road abuse much better, being the more silent and smoother ride.
IST was more responsive , fun to drive and also looked better vs the Vios. But i think Vios had more pick up.
IST had a few grades, where you got some very good kit for the car. (F, FL so on). Personally if you ask me i would prefer the IST , against the Vios , during the whole usage experience of mine.