Performance of 1.5 is way better than 1.3, secondly if you want to have auto you must opt for 1.5 otherwise 1.3 AT would be underpower.
As per my little experience, a slightly bigger engine gives you long lasting performance.
I have a 2003 civic exi manual 216000 kms driven and Honda 3S maintained and she gives me 13km/l in city these days wo AC. On long routes she gives 17km/l on highway @100-110km/h wo AC and 15km/l with AC.
Whereas my father have got a 2012 Gli 1300cc only 10800 kms driven and I took her to Islamabad twice last month and she hardly did 14.5-15km/l @ 120km/h and rpms are 3.5.
If you have to drive frequently on highways and motorways 1.5 would be better otherwise you can opt for 1.3 MT.