суп and рис are accusative forms. Feminine nouns ending in а or я have different endings (у or ю, as you said), but masculine have the same form as nominative if they refer to objects and inanimate things and genitive form if they refer to living, animate things. All other feminine and neuter also stay the same as nominative.
When someone uses the wrong ending - how difficult is it for Russian-speakers to understand what's being said? English is extremely flexible in that one can still be understood despite doing terrible mutilation to the language, and I'd think that Russian has some great degree of flexibility in it that way, especially since many vowels don't seem to be pronounced the way I was expecting them to be, under the general rules. I assume there are regional variations akin to the difference between being from the North and South of the USA.
I'm guessing based on what appears to be a prefix при- (maybe) = English "pre-" that приготовить means to do everything you need to do to get things ready to cook (slicing and dicing, etc.), while готовить refers to both the entire process and to finishing the cooking process. In US commercial kitchens, people are assigned to "prep[aration] work" and then actual cooking, but the whole process is cooking. Seems logical.