Really depends on your child's disposition and the time of the year you're traveling.
Agree with getting rid of night near Mt.Fuji.
I'd spend the first 5 nights in Tokyo. I think a day trip to Nikko is fine, as long as you're taking one of the limited express trains with reserved seating to/from.
Harajuku, Akihabara, fish market... seems like a lot of activities in one day. I've not been to the new fish market in Toyosu and don't know how that works but, if that involves having to get there at the crack of dawn, then your kid's probably going to hate it (I would hate it, too).
If you decide to go to Hiroshima, if it were me I wouldn't take my 2.5yo child to that Peace Museum which has a lot of depressing exhibits.
Miyajima is wonderful. I think a trip up Mt.Misen on gondola is almost a must if it's a clear day, and then you can further climb up to the very top. That climb is very easy but still probably a bit much with a 2.5yo in tow, though.

In many sense, traveling with a child gets a lot easier beyond ~2yo when you're not using the stroller anymore. But most 2yo's aren't going to be able to walk too far or sit too long (limited express trains are fine, since your child can lie across your/spouse's laps, walk around, etc), and some still need nap time. I think you have to take all of that into account in your planning.