Resale of GLi AT is equally good as that of GLi MT. I had put my GLI AT Sept. 2014 registered for sale in January 2015 and got offers for more than my cost including registration. After that i placed ad for sale last month just on pakwheels and olx and got offers close to my cost including registration (declined sale due to oncoming civic and restrictions from my employer for change of vehicle under loan term).
However in term of power it is a bit different story. As a utility it fulfills all purposes, has very smooth automatic gear but for pick it is behind GLi MT. Power is not there at the right time when you floor it. You have to build momentum to overtake at highway. On the other hand it is very comfortable and smooth in city start stop driving.
I have driven new 1.6 Altis extensively, and i feel it is marginally better than 1.3 AT not a very huge difference. At highway, being automatic gear, 1.6 altis also does not gives you instant power when you want overtake a lorry. If IMC would have introduced manual, 1.6 altis would have been a big cheer on anyone's face. Moreover, you also have to consider resale value after 1 or 2 years for 1.6 altis.