Please go through below thread, It had detailed discussion. Yaris have 7speed (virtual not physical) gearbox not engine.
Altis 1.6 have better shape, more powerful, excellent resale, compact sedan (yaris is subcompact) and definitely FL look awesome. Downside is 4pd transmission which result in low fuel economy. But this gearbox is more reliable and solid than CVT.
Yaris have more frills and feature and slightly better fuel economy. IMO if budget is not an issue, Altis 1.6 is better choice overall.