Hi JL,
Flexi season tickets are not an option within London because daily caps are already 1/5 of the weekly cap/travelcard. The daily cap for zones 1-6 is £14.10 and will be reached if two peak time journeys are made. It doesn’t really matter which route you take. One option you may not have considered is Kingston – Wimbledon – Farringdon – Barbican/Moorgate. This may be slower on the travel time, but cuts out long walks between trains at Waterloo and wherever else you change on the Underground. Both Wimbledon and Farringdon are simply crossing a footbridge, and on the way home it’s adjacent platforms at Farringdon.