You may find complete information about different Toyota Vitz variants here (based on prices and features), and then compare them:
https://jpcenter.ru/m?name=catalog&mnf_id=1&mdl_id=9580
The most common package in 1000 cc is F package, and now, 1500 cc hybrid variants are also being imported (although rare).
With regards to performance, 1300 cc variant will definitely always out perform 1000 cc equivalent variant. 1000 cc Vitz feels quite under-powered. The duty structure is so high that no 1300 cc / 1500 cc Non-Hybrid variant is now being imported.
Fuel efficiency of 1300 cc is almost same as that of 1000 cc, and 1300 cc gives best balance between pick, power, performance and fuel efficiency.