Copying this wonderful analysis of 1.3 AT vs 1.6 AT by @nido747
Every body will guide you their own way, it is YOU who has to decide which tranny should go for. I am going to give you my incapable opinion.
I will suggest you to go for 1.6 if your budget allows . The Things that you mentioned, i will try to answer these one by one.
(Altis 1.6 has no 1.8 equivalent features besides alloy rims.)
Altis 1.6 has alloys as you mentioned, nav ready infotainment system with back view camera, Hi Grade fabric seats as mentioned on indus website (Please see),Extra two color Super White and Bronze Mica if you want to opt that and above all dual VVTI 1598cc bigger Engine. you can get after market alloys, infotainment system in the price range of 90k (125k-90k= 35k) but you can't replace 1.3 engine to 1.6 engine in 35k.
(The fuel economy is worse than both 1.8 n 1.3)
It has dual VVTI engine as compared to Single VVTI engine in GLI A/T.
The engine on the 1.6 is not just bigger, it's newer and more efficient both in terms of fuel consumption and power output. NZ-FE(1.3)VVTI series vs ZR-FE(1.6)Dual VVTI.
The transmission on both is 4 speed super ECT but it's not the same. The 1.6 has an Aisin Warner (one of the world's top transmission manufacturer) A341E original japanese transmission. The 1.3 has a toyota U341e which to the best of my Knowledge is from Thailand. The A341E is much smoother and more reliable. Also to consider is that the u341e is designed for 1.5l engines, not 1.3. It has a first gear ratio almost 1.5 times that of the first in manual gli and a second gear ratio equal to what would be a 2.75 gear of the manual while the third is equal to the fourth on the manual. That is why the 1.3 gli AT is significantly slow off the mark as compared to the gli manual. AT is always slightly slower than manual but the difference is quite significant here. The same specs go to the advantage of the 1.6 as the more powerful engine utilizes the lager gear ratios for a more rapid off the mark acceleration and even slightly better fuel economy than the competitions slower 5 speed with a 100cc smaller engine.
So if it's automatic you want, the 1.6 is worth the marginal extra cost. Otherwise settling for the 1.3 city AT (if you dont mind it's other design flaws) or the gli manual would be better.
(The 7" lcd in 1.6 Altis has no DVD disc option with no navigation (separate card for rs 14000) )
Neither 1.8 Altis has DVD disc option. The reason is, did you ever see cassette players in any new car Local made because they become obsolete. Now these DVD discs are also getting obsolete and instead usb is taking their place. You can have around 64 GB usb and you can put around 64 disc data/Songs in only one usb. Altis 1.6 infotainment System is Nav ready and yes separate Nav card is needed but most of 1.6 Altis owner made this nav card FREE by their own by following @autophile Thread. Autophile Sir made this free card by his own and it is running flawlessly and i am also using this card.
(The GLI 1.3 ( 9" navigation system can be bought by paying additional 40 k with DVD option))
You know the quality of aftermarket Chinese product.
(The GLI audio player can be refunded to toyota for RS 5000 while Altis 1.6 screen cannot be exchanged)
only if you buy from Dealer. They will give you higher price of infotainment system as compared to local market and they are getting 1.3 DVD player almost free.
(Recommended GLI as ur not racing around on crowded roads of karachi with 1.6l Engine)
It means that no body from karachi should buy Altis 1.8 or 1.8 engine should not be present for karachi people.
(Help me guys i wanted 1.6 altis as i thought 1.3 gli would be underpowered which may lack driving pleasure)
I do not believe that 1.3 Gli is an underpowered car . Many pakwheeler friends are satisfied with their power (you can see @fouadbakht bhai and @aliusman420 bhai thread . I didn't drive 1.3 Gli A/T 11 gen but i think 1.6 drive will be more joyful as compared to 1.3 drive due to their gear ratio.
This is my opinion, hope it will help you in buying your car.
And I add: You will love the way the 1.6 AT launches and the thrust of engine as you press the gas pedal is priceless. Gli will never give you that feel and superior power drive.