Using a trailer when needed may be the way to go for you. You might be able to haul both kids on the Minute by putting the daughter on the back and using something like an iBert for the little guy once he can hold himself upright in the seat.

It's hard to beat a true cargo bike (e.g. longtail) if you are going car light/free. I find mine much more practical to use than my trailer. But if you have much of a commute, you would probably want to supplement that cargo bike with something lighter and more traditional. I love my Yuba for what I use it for, which is several times a week, but I would not want to be limited to only having it for commuting puposes.