Fresno native here - I concur with the 3 park scenario.
Enter Yosemite Valley via the west gate, and then exit the park through the south gate at Fish Camp. Spend one night in Fresno, have dinner at one of the Basque restaurants that serve big family-style dinners (I like Shepherds Inn in the Downtown area).
Next day, head over to Kings Canyon and Sequoia.
You'll have a more relaxed pace to enjoy your vacation, and the toddler won't be burnt out.
Also if FAT airfare is too high consider SJC - closer than SFO.