I too was caught in this dilemma, but booked Gil 1.3 Manual as AT deliveries are in June for this variant. But after two weeks I changed my order to Altis 1.6 for the following reasons.
A difference of just 220,000 rs but you get. You can get rims and DVD in any car, but cannot change engine (of a new car).
1- Dual VVTi engine 1.6 litres
2- Auto transmission
3- Alloy rims
4- LCD with reverse camera
5- Choice of Super White and Bronze Mica colours which are not available in Gli AT (though I opted for Med Sliver :))
Annual token tax is not much, it is just like 1.3 City.