If you don't mind spending for the over night stay I'd do that.
We did the Ephesus only trip and the journey was horrid. Ephesus is lovely when you're there but it's actually getting there that's the chore.
We were peed off we had to stop off at some pottery place for over an hour before we got there then when you get to Ephasus you're only there an hour and 45mins and it just isn't enough time at all IMO. I'd have gladly missed the pottery place to spend more time in Ephesus.
I went off on my own with the camera, we'd have missed so much had we stayed with the guide, everything was so rushed. When we got to the Library (breath taking) we were told we had 15mins we hadn't even got down to it and making our way up the step and we were being called back.
Oh and a tip, sorry I can't remember the correct name of it but there's a street that's being uncovered (you can't miss it it's all under cover before you get down to the Library) BUT you're not allowed in there if you're in a big party - slope off away from your guide and have a look it's meant to be fantastic your Son will love it.
Take plenty of water and a cap/hat as it gets REALLY hot there and there's no shelter. I'd recommend taking a little cooler bag if you can squeeze one in your case and take as many frozen bottles of water as you can fit into it as you can. I'd also take some snacks too as the food at the lunch time stop isn't very nice at all. You don't have to take everything off the coach each stop so take what you can.
AND another tip if you go to the museum instead of the Virgin Mary's house do NOT let anyone shine your shoes. Hubby got caught on the way out, he kept saying no and the guy's saying no shoe shine no shoe shine it's ok then tried to fleece us 10lira for wiping the dust off his sandals - I took off with our money off hubby and the guy got really nasty. He got 2 lira as that's all hubby had in his pocket