According to Levenspiel (Chemical Reactor Engineering, 3rd ed, 1999) batch and continuous reactors have advantages and disadvantages. Choosing the best reactor will depend on the physico-chemistry of your effluent, the easiness of process control, primarily by the volume of liquid waste to be treated by the hour or day. Batch reactors are preferable when:
1) treatment has reduced scale,
2) safety hazards,
3) slow reaction kinetics or low performance treatment,
4) low volume of effluent to be treated
For more information search this book (Levenspiel). Good studies,
SBRs are best suitable for low wastewater volume, needs to be automated (cycle control), better for high load and to control filamentous growing (in highly degradable wastes), not suitable for wastewater containing toxic substances (no possiblity to equalize the toxic load to appropiate levels). It works like a plug flow reactor in time instead of space, so it basically has all the advantages of this kind of flow.
Continuos reactors on the other hand can be design to work in complete mix regime or plug flow and are best for higher wastewater volume.
Anyway, to answer your question about which one is more often used: continuos reactors.