Skoda Kodiaq

While the Toyota Fortuner has strong road presence and a powerful image, it does not offer a premium and sophisticated experience that is expected of the price. 

The Skoda Kodiaq would be a better choice as it has the right level of premiumness and performance, and is a lot more comfortable than the Fortuner. Mileage numbers will be similar for both SUVs, but the diesel engine in the Fortuner would be a bit easier on the pocket. 

Our recommendation would be the Skoda Kodiaq as it offers better value and is a better product overall. 

You have correctly identified each SUV's weakness; thus, it really boils down to which of these is the least worry for you. On the whole, the Skoda Kodiaq is something you could consider, unlike the other car's weaknesses. 
Also, you could offset the lower AC performance of the Skoda with good habits like parking the car with a sunshade and also using window blinds.
If you are open to looking at an EV, we would recommend you look at the Ioniq 5. It isn't a three-row vehicle, but it addresses all of the weaknesses you have mentioned in the other cars in your shortlist.  

The Skoda Kodiaq and Toyota Innova Hycross are very different products, and your choice depends on factors you'll give more weightage to. 

The Skoda Kodiaq is significantly pricier but offers a significantly more upmarket interior. Interior quality is as good as many luxury cars, and there are lots of features and goodies packed in, too. The Kodiaq is also the more entertaining vehicle to drive. Its 2.0-litre turbo-petrol engine delivers strong performance, which is something you'll appreciate when you drive. Rear seat comfort is good, but the Innova Hycross has the edge here. 

The Innova Hycross has a roomier cabin, and the middle row seating is more comfortable. The legrests on the captain seat versions count for a lot to up comfort levels when you are sitting at the back. Also, thanks to the strong hybrid powertrain, the Hycross is significantly more efficient than a Kodiaq. Also, purchase price aside, regular maintenance in the long run will also work out cheaper on the Toyota. On the flip side, while the Hycross' EV mode is unique, the Toyota is essentially unexciting to drive. 

A Skoda Kodiaq is better equipped, more spacious, and it is more powerful than the Mercedes GLA petrol. A Volkswagen Tiguan R Line is also something you can consider, which is a bit sportier to drive than the Kodiaq, and now with huge discounts, is a tempting option.

The Volkswagen Tiguan R-Line is enjoyable to drive but is undoubtedly expensive. Regular maintenance should not be a problem, but the availability of parts could be an issue in case of accident repairs. Expensive imported cars also typically do not retain their value unless there is special market interest.

As an alternative, consider the Skoda Kodiaq, which is essentially the same car underneath but offers more features and a generally plusher interior. Parts availability will also be better for the Kodiaq.

If driving experience is a priority, the Audi Q3 is also worth considering. It may not be cutting-edge inside, but it is engaging to drive with a strong petrol engine. With the next-generation Q3 expected in India next year, you could push for big discounts on the current model.