Is Marienplatz worth a visit? Yes, IMO. It is the hub of the Altstadt. Take the lift up the Rathaus and get a glimpse of the alps or a close up of the Frauenkirche. Visit the Viktualienmarkt and Der Alter Peter church, not to mention Dallmayr Deli - I return just for the Christmas chocolate bars. By sticking close to the center, you can set your own pace, and transportation options are plentiful. The recommendation of Freising sounds good to me, too.
If I found myself in Schwangau, which has happened, I would opt to see Hohenschwangau rather than Neuschwanstein. Much more interesting (to me) with the furnishings and knowing folks actually lived there. Plus, you can take lots of photos of Neuschwanstein. If you do go, there is a nice restaurant on the lake with outdoor eating.
Still, it is a lot of effort at the end of a long trip. Staying in Munich may be more relaxing, less hectic.