The main differences are :
1.5L engine
Smart entry
Mid and cluster
Push start
Trunk opening button under the garnish (just like civic oriel)
Navigation with rear camera
Climate control
Chrome door handles (both outer and cabin door handles)
DRLs (it will be available soon in market for hardly 6 to 8K rupees )
To be honest you should go for top of the line variant as you will be getting so many things in just 250K (if you plan to keep the car for longer period of time atleast 2 to 3 years)
Now why am I going for Ativ 1.3 ?
Out of all 6 variants, 3 variants will have a good future
1. Base variant M/T
2. 1.3 Ativ CVT
3. 1.5 Ativ CVT
And if we look at these 3 variants, 1.3 Ativ CVT will have best resale value. Premium will be highest on this variant as well.
Lack of power retractable mirrors in top of the line variant is a deal breaker for me ! I really like all other features but still this was a must for our tight and congested driving conditions. Furthermore I am not exactly sure but I am really interested in getting New Hyundai Elantra and this particular variant of Yaris wont give me any loss if I decide to dispose it off in 6 months to get elantra or in 1 year to get new Corolla. It is a good car with all necessary features, there isnt any big difference in performance and power if you compare 1.33 ltr with 1.5ltr. I really didnt like the navi panel of 1.5 ativ and in any case I would be getting an aftermarket android player. Now finally if you calculate on road price of the car including insurance then again 1.3 Ativ CVT makes more sense you will end up spending 28lacs on this car which is the max limit for a car of this category, if you go for top of the line variant it will cost around 30.5 lacs which is a bit higher for a car of this category. You can get a really good well maintained Civic Oriel 1.8 2017 in this price.
1.3 Ativ CVT has almost everything except a few good features like push start and smart entry and you can live without that. Plus I have a 1.5L hybrid and 2.5L V6
and both of them have all these features infact many many extra features as compared to 1.5 Ativ so its ok to have a car without push start thora chaabi ghumanay ka dil hora hai kafi time se nae ghumai 
But I will say again, if you plan to keep it for long and this is the only car you have or if this will be the best car in your garage then it should have all of these features so you should get 1.5 Ativ.
Best of luck