Your pediatrician is probably making the recommendation to stop the bottle and take away the pacifier because it can be more challenging if you wait until later. Some also believe leaving a bottle/paci in their mouth at night can lead to teeth issues. But you have to do what works for your child and you. My youngest daughter is now 14 months old and she still has the pacifier at naptime and bedtime. She does still nurse and takes all cow's milk and water from the sippy cup now. I have 4 children and my oldest 2 are already in elementary school and they have never taken a bottle or pacifier with them to school...point being...you'll work it out when the time is right to take it away and kids grow up just fine. None of my children have had a single cavity to this point and none of them are buck-toothed either. You don't have to be rigid about it or cut your baby off cold turkey. That will just be stressful for you and for your son.
As for switching from formula, that's a standard thing and my only advice is to be willing to try 2% chocolate milk if your child doesn't like white milk. I have given all 4 of my kids chocolate milk at 1 year of age because I exclusively breastfeed, which naturally tastes sweeter, and so my kids never would take the white whole milk. None of my children bounce off the walls any more than normal and none of them are overweight either. Instead of formula, your little person should be getting plenty of nutrients now from the foods he eats anyway.
I would also check into another pediatrician if you're not comfortable with your current one. If you frequently question his advice, don't trust him or don't like the way he speaks to you or handles your child then it's time for a different Dr. I do think your Dr. was ultimately trying to help and give you sound advice but it's always best to go with your motherly instinct. I trust my pediatrician with matters of health, nutrition, vaccines, etc. but knowing what my baby likes and what makes her comforted is something only a loving Mommy knows best. So for now...we are keeping the pacifier and I'll just limit it for use during bedtime/naptime. Best wishes!