just returned from a trip with DD2 and stayed on the monorail at the Poly, and I have to say, with a child that age, it was definitely nice to be that close to the room when we were at MK. Using the buses from AK would add at least an hour onto your total day in roundtrip travel, more if you go back for naps, and half of that longer voyage will take place when your little one is already spent.
It ultimately comes down to what is most important to you, of course, but we plan to stay at BLT while our daughter is still very young. With that said, I can totally see the draw of having animals outside of your room for a small child as well, and for that reason, we might split our stay between the two and do a couple of days at AKV for the days that we plan to be over there. When you're spending a lot of time at MK, though, it's tough to pass up that convenient location with a child that age, IMO.