Need advice

Our family is currently looking at getting our first car. We settled on getting an Avanza 1.3 E CVT or Avanza 1.3 E MT, and we are wondering if it would be better for us to get the MT or the CVT.

Considerations:

1. We mostly do city driving (school, palengke, mall, office), with some highway driving
2. We also pass through floodprone areas (half wheel height). We do not know whether it would be better to have a CVT or an MT for those rare moments.
3. We are also looking at future maintenance expenses that may arise.