For the most part I think you will just have to see what works for you. My daughter will be 1 in 2 weeks and I have been giving her naptime bottles of 4oz of goats milk (local, organic and I think it tastes better than cow milk) but I still give formula for bedtime when she needs a little more nutrition to help her sleep through the night. She has been drinking formula from a sippy cup for a while since I don't take a bottle with us when we go out, so if we are not home in the afternoon she gets it in a sippy. She seems fine with milk in the sippy too. She has a history of giving things up as she is ready (swaddling, pacifier, etc) so I will let her take the lead when it comes to weaning from bottles for sleepy time. I ONLY give her a bottle at nap/bedtimes (I've started skipping the morning bottle and just giving her milk in a sippy and breakfast) and I NEVER leave the bottle with her. She sits in my lap and has her bottle, then goes in her crib, hugs her lovey bear and sucks her thumb to actually fall asleep. I figure that no one would think twice about breast feeding for bedtime/naps and comfort after 1 yr old so why give up the comfort and intimacy of having a bottle at sleepy time? I'd be more concerned if she needed her bottle all the time in public and to actually go to sleep, but that's not the case. When I stopped the morning bottle she didn't even notice.
Oh, edited to add that I only mixed the milk w/ formula for a few days just to make sure she didn't get any digestive issues from it. Once I knew it wasn't bothering her I gave the milk to her straight. She doesn't seem to notice or care whether it's formula or milk.