Itinerary help for Bavaria in Late Sept 2020

Do you already have lodging reservations for Munich during Oktoberfest ?

You'll want to stay away from Munich if at all possible, as rooms are high season. I like doing a circle around Munich in a counter-clockwise rotation. My first stop would be Andechs to visit their brewery--one of the best beer halls of them all.
www.andechs.de/en/brewery
Then you could go on south to Garmisch, east to Innsbruck and back around to Salzburg. (I'm personally not big on Fuessen or Neuschwanstein.) You could catch Munich at the end of your trip.

I like the Garmisch-Partenkirchen suggestion as it is a picturesque town nestled in the Alps. From there, you could easily ascend Germanys' highest mountain, the Zugspitze, via cable car or mountain train (I suggest cable car) as both the ascent and descent provide spectacular views, providing there is good visibility. If you have never been to Neuschwanstein, I would definitely put it on the itinerary and there are several hiking opportunities right near the castle. I suggest a stop at Linderhof, King Ludwig II's "hunting lodge" as it is not as crowded, but nevertheless beautiful. Be sure to visit the Grotto up the hill. Next year is the Passion Play, which takes place every ten years in Oberammergau, which might make things more crowded than usual. Salzburg is a beautiful city that is definitely worth two nights.

WE do not already have accommodations in Munich yet. I am sure that it will be crazy due to Oktoberfest, but a limited stay is what we are looking for there. I have not explored lodging yet for any of the trip really. Wanted to try to figure out an itinerary first.

We will be going to Oktoberfest in September and we are staying near Garmisch. We will take the train to Munich on our Oktoberfest day. We've been to Munich before, so staying further away works for us. We went to Oktoberfest in 2010 and stayed out of town and took the train in that time as well. Munich itself will be €€€.

We are also going to Munich for the 1st week of Oktoberfest and are staying in Freising, stayed there previously and is a very easy commute to Munich

"We are having trouble deciding on where else to go (too many options). Considering some time in Mittenwald, maybe Fussen, maybe Salzburg?"

I would pay close attention to Andrea's post. It's only 1 hr. 20 min. by direct train from Garmisch to central Munich (this is nothing you want to try by car, btw.)

If you pick Garmisch, you do not have to decide on your sightseeing options right now. It's a very short train ride from G-P to Mittenwald (must-do IMHO.) Füssen, the Wieskirche, Ettal Monastery, the Zugspitze, Linderhof Palace, Oberammergau, and other sights can all be visited by local public transport on day outings from this handy base town.

It's possible you will enjoy Garmisch's Fraundorfer Inn atmosphere more than O'fest.

Why not book a few days in G-P AND a few in Salzburg? Salzburg is a great choice too and a good travel base - and you have similar outings available to you that can be chosen later.

Hohenwerfen Castle
Berchtesgden
Eisriesenwelt Ice Cave experience
Herrenchiemsee Palace (on the way to Salzburg, on an island in Lake Chiemsee.)

An option to consider: Garmisch for 4 nights, Salzburg for 4 nights, with a one-night stopover in Munich for O'fest either in between or at the very end.

It might not be necessary to stay over in Munich at all... On Day 5, leave Garmisch early for Munich, drop bags in a locker, stay there all day for O'fest, and arrive in the PM in Salzburg (by TRAIN of course, assuming your O'fest includes some Bier!!.) Then stay your final night near the airport in Freising, a nice place that's already been suggested.

I don't think you can miss by staying in the Berchtesgaden area (Schönau am Königssee, Ramsau bei Berchtesgaden) and take a day trip to Salzburg and a second on the Königssee, Nationalpark Berchtesgaden (electric boat to St. Bartholomä and Obersee ) and time allowing Berchtesgaden. The new Jennerbahn is open too. A car gives you a little more freedom as to how far you can roam. You can use Park & Ride near Salzburg (euro 15 for parking and 5 folks on the bus). Two days give you some weather flexibility. You can check out famous calendar views like The Waltzman from Berchtesgaden and Schönau, Malerwinkel in Ramsau and The Wallfahrtskirche Maria Gern etc. I like to stay at the Gasthof Auzinger near Ramsau when open (almost in the Nationalpark Berchtesgaden). They have live Bavarian music on Wednesdays, but please check ahead.
https://www.ramsau.de/webcam-malerwinkel.html

If you do the Garmisch to Innsbruck to Salzburg loop, there are excellent hiking opportunities in the Zillertal just southeast of Innsbruck.

Zillertal.at

We would like a mix of active activities (hiking and biking) as well as more leisurely things (we love good food/beer and wine). Considering some time in Mittenwald, maybe Fussen, maybe Salzburg? Any suggestions on places to not miss?

Everyone here already has some great suggestions but I'll throw in one more: Tegernsee.

This is s good lake/alps/villages combo close to Munich so you won't spend a lot of time in transit plus you can easily get back into town if you want to hit the Oktoberfest tents. It can be accessed from Munich using the BOB train (they have a combo BOB-MVV ticket). Since it is a touristy area there is a lot of good infrastructure for visitors. The lake has several small villages surrounding it which are joined by bus (free with a tourist card if you are staying in the area), a foot/cycle path (easy to rent bike to ride around the lake) and ferries across the lake. There is a great Brewery/Restaurant right on the lake, Bräustüberl Tegernsee. Lots of good hiking in this area as well. If the weather is nice you can take the cable car up Wallberg and hike to a hut in the mountains for nice lunch.

Here is another thread with lots of things to do in Tegernsee: https://community.ricksteves.com/travel-forum/germany/things-to-do-in-tegernsee-area

If you are really into hiking, I would suggest checking out this website. It is where people post their favorite hike/bike/xcountry ski routes (sort of like mapmyride). It gives you lots of info on times, distances, elevation and difficulty.

DJ

Edit: I'll also add my suggestion in for Oktoberfest accommodations. If one of the Motel One locations has rooms reserve them now even if you are not 100% sure you will use them as you can cancel up to 3 weeks before your stay. I like the Motel One Ost, Haidhausen or Sendlinger Tor locations.