Very broad question. Depends on what fruit species you are interested. What about seedless mango or durian without that smell some people don't like? For any fruit species canopy management is important but then apple has dwarfing rootstocks. No suck luck with mango or rose apple so far. Colour, unique shapes and improved antioxidents..so many objectives to think about but you may first want to narrow down on the species and two or three most important characters.

major fruit crops like Mango, Banana, Grape, Guava

Hi

I think that working on extending production season (early and late cropping) is always welcomed.  precocity traits are also important. storage and transport related traits are also very important (especially for the mentioned fruit trees). last but not least adding resistance characteristics toward biotic and abiotic stresses is a common thing.

each one of these traits have its methodology that can be followed to achieve the purpose of the program.

best regards