We did an 8 day trip and stayed in an apartment one stop away from DLP. We did what you are suggesting and got annual passes. At the time my kids were toddlers (twins just under two at the time) so I wanted to be able to leave and go back if I wanted. They did well sleeping in the stroller so we never needed to go back, but I had the option.
I live in California so everything takes 30 minutes so the commute into the city didn't bother me, just don't miss the last train because it would be an expensive taxi if you miss it. Non-Disney hotels/apartments in the DLP area were a lot cheaper than the city. Versailles was difficult to get to, but other than that most things we could get to easily with public transport. You do not want your car in the city. Like the other poster suggested, if you want to explore other areas outside the city get a car.
I assume you have not been to Paris before, but you could easily spend 12 years in Paris and not see it all. Your plan to mix it up is a good one.