The waking intervals are perfectly normal. He is still an infant. My son is two and a half and still wakes usually once per night - but woke at least two to three times per night until around the time he turned two. Thirsty, hungry, needing to eliminate, reflux, heard a bump in the night, looking for mommy - all typical reasons for an infant or even young child to wake during the night. This time goes by SO SO SO fast, you have a two year old, so you know how quickly they grow out of infancy. It won't last forever. You will get to sleep again! ;) The most important thing right now is forming a bond with your baby and teaching your baby that he can trust you to meet his needs.
As a lactation counselor, I would never encourage 6 ounce feeds of either breastmilk or formula at that age. BUT I say that to say, your son is not obese (I'm actually chuckling at the pedi saying that - they really are not infant nutrition experts, even if they speak as though they are). But, he does need to be fed if he is crying to be fed. Ignoring an infant's cries is just not necessary for proper development, in fact there are a number of recent studies that have shown actual cognitive delay and attachment issues as a result of having their cries ignored.
As for sleeping through the night - ALL babies are different. And there are SO many variations of STTN as well, and so many reasons for it. Some babies don't need to eat as much, some have been left to cry it out, some just have their own sleep cycles, some are overfed before bedtime, some have a pacifier to keep them content when waking, some are just generally less "needy" overall...
Suggestions for you that don't involve ignoring his cries:
Try (very quietly) changing his diaper and rocking him back to sleep when he wakes - if his cry becomes more intense, it is likely he is hungry or needing to suck, so feed him.
You could try a pacifier, if you haven't already, if it were a sucking/comfort need that could help with that aspect.
If you do feed a bottle, make sure it is paced fed - yes it will take longer, but it will keep from overfilling/stretching his tummy. Start with a six ounce bottle since that's what he's used to, but don't hold it at an angle where all he can do is swallow as he sucks - the sucking part is absolutely instinct, and the swallowing is a defense mechanism - he can't tell you he's full, he wants to suck, but he doesn't know he doesn't need all that formula/milk, so he keeps having to swallow it to keep from drowning basically. When people say a baby knows how much they need to eat ... well ... sort of. But since humans were built to get milk from a breast, which is actually very hard work for newborns and young infants, a bottle on the other hand is very easy to get milk out of, and so they tend to overeat on accident. So, definitely feed as much as he wants, don't withhold food, but allow him to determine the pace at which he eats, and the quantity - give him frequent breaks, hold him sort of upright, hold the bottle so he has to work to get the formula out of it - those will help him regulate his food intake as nature intended.
And, lastly, the thing I tell all of my clients to remind themselves - he spent 9 months inside of you where temperature was stable and warm, he had a constant food supply, frequent motion, ability to pee comfortably, and was always being "held" .. he's only been in the real world for 3 months, and in that time has experienced silence, cold, hunger, the feeling of clothes, wet/soiled diapers, being alone, and so on and so forth. He's still in adjustment phase, and will be for awhile. Even if he's waking because he needs the comfort of his mommy, that's a perfectly okay thing to provide him in the middle of the night. <3