Congratulations on getting married!

Really, possibilities are endless as far as where else to go in Jpn. There's lots to see in both Hokkaido and Kyushu. I'm sure you've only scratched the surface in Tokyo and Osaka.

Honestly, though, I think it's probably difficult to imagine what would interest your whole family 2-3 yrs from now when you have a 2-3yo child. Everything changes when you have a child. Everything starts to revolve around kids. Your trip planning, what to see/do, where to go eat, what channel you turn on on hotel TV, everything becomes centered around the child. Before my kids were born, we'd do long hikes, watersports, intimate restaurants, hit up bars and izakayas, be out for 14hrs at a time, change hotels daily. With kids, each vacation day is much shorter, there's the stroller, we're doing Kido-kido (indoor play facilities in Jpn), Anpanman Museum, Kidzania, parks and trying to select hotels/ryokans with buffets (cuz that's what works best with our kids).

So I'm probably not helping you much, but I think it may be premature for you to be able to start doing any definitive trip planning. I realize this doesn't apply to all married couples, but I know it applied to us and to probably majority of parents. But for us, three things that remained constant in terms of our travel themes before and after kids were: beach, food, onsen.