Normal wear and tear for the automatic transmission should be expected especially if you keep the car long.
However, you could somewhat decrease the number of problems that might appear in your transmission if you just follow it's maintenance.
If you really want a 1.5L vehicle in M/T form at the same time, cheap then you should be looking at the Toyota Yaris by now or the Toyota Vios 1.5M/T. The location of the instrument panel of the two is somewhat, not attractive.
If the Jazz however is you last bet then I guess you could just opt for the 1.3L instead. It's transmission is manual so I guess it wouldn't be really underpowered unless you fill it up with heavyweight people + baggage.