We had (or, my wife had) kids m1, fall of my and intern year. A few thoughts -
*Morning sickness - for some women it's nothing, others have a terrible time. A classmate of mine passed out and had to get sent to the ed at one point for dehydration.
*family help - makes all the difference. Spouse at home =much easier. Family within short driving distance still helps. If you and dad both work terrible hours and no family help - better rethink having kids or, if you insist, have a good nanny.
*As others have said - baby can decide to come early or there can be complications
*I was exhausted for the first 6 months after my kids were born, and I didn't even feed them in the night - but I think that first 6 months is the worst, after that they start sleeping and things settle down a bit.
*it's hard to plan a baby. We tried, had miscarriage, threw off our plans. Had baby during "not ideal" time (internship), is hard but doing ok.
My $.02 - end of 3rd year is tough. I'd be prepared to miss at least one rotation and make it up in 4th year. I'd think early 4th year would be easier - if you're not going to have to do audition rotations. If your going for specialty which requires auditions, I might wait until early spring 4th year.
At the end of the day, let your professional life inform but not run your family life. If it's time to have a kiddo, have a kiddo! Just realize what you're up against - and, when choosing a specialty, reflect on how this may affect your ability to be a mommy. Lots of people can take care of a baby, but they only have one mommy ...