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I need some help making choices for a 10 day, 11 night trip to Bavaria and the Swiss alps, flying into Munich in the last week of August and flying out September 3.

I am interested to see a little bit of everything: nature, historical sites, quintessential towns, and castles. In Munich I'd like to see Marienplatz, churches, beer hall, and some museums as time allows. I had some interest to hike in the Bavarian Alps since there seem to be some lovely hikes, but based on my timeline I think time may be better reserved for the Lauterbrunnen Valley. I'm still considering a trip to Berchtesgaen, however. For me, Neuschwanstein is a must. Which Bavarian town I go to isn't terribly important, although I listed some I think look interesting to me from my research; location should be strategic time-wise, and I need to be able to get to Innsbruck from there.

I have two primary ideas I am working with:

Idea A involves 1.5 days in Munich, 1 day in Salzburg, 1 day in Berchtesgaden, 1 day seeing Fussen and Neuschwanstein, 1 day in Ettal or Oberammergau or Mittenwald or Innsbruck.
DAY 1 - Flight to Munich lands 1 PM, Half day and spend the night Munich.
DAY 2 - All day in Munich. Spend the night Munich.
DAY 3 - Early train to Salzburg. Spend the night in Salzburg.
DAY 4 - Early train or bus to Berchtesgaden/Eagle's Nest. (Logistical aside: place to store bags?). PM transfer to Fussen (public transport option?). Spend the night in perhaps Fussen/Ettal
DAY 5 - See Neuschwanstein and Fussen. Spend the night in perhaps Fussen/Ettal
DAY 6 - Choose a town to see: Ettal or Oberammergau or Mitenwald during the day. Spend the night in Innsbruck.

Idea B involves 2.5 days in Munich, 1 day seeing Fussen and Neuschwanstein, 2 days seeing castles or towns such as Linderhof, Ettal, Oberammergau, Mittenwald, or Innsbruck.
DAY 1 - Flight to Munich 1 PM, Half day and spend the night Munich.
DAY 2 - All day in Munich. Spend the night Munich.
DAY 3 - All day in Munich. Spend the night Munich. (or this could even be a half day in Munich, night elsewhere)
DAY 4 - Early train or bus to Oberammergau or Ettal. Spend the day seeing these towns. Spend night in Fussen.
DAY 5 - See Neuschwanstein and Fussen. Spend the night in perhaps Fussen
DAY 6 - Train or bus to Innsbruck, or AM one more town or castle visit, then half day in Innsbruck. Spend the night in Innsbruck.

In either of the current itinerary options, I imagine the trip would end as follows:
DAY 7 - Earliest AM train Innsbruck to Interlakken. Enjoy the views as the sun rises. Transfer Interlakken to Murren to arrive in the afternoon. Spend the night Murren.
DAY 8 - Hike around Murren. Spend the night Murren.
DAY 9 - Hike around Murren. Spend the night Murren.
DAY 10 - Earliest AM transfer Murren to Interlakken. Train Interlakken to Zurich. Half a day in Zurich Old Town. Spend the night Zurich.
DAY 11 - Late morning flight home from Zurich.

What I'd particularly like help with is deciding whether or not it makes sense to travel East off the Munich-Zurich path to Innsbruck and Berchtesgaden (Trip A), or whether it involves too much transit time, not enough time for sites. I should include that I tend to travel willing to wake up early and go to bed on the early side to maximize time.

Any feedback on the best way to design the itinerary is appreciated!

to look up trains schedules see www.bahn.de/en - German railways site for all European trains. In Bavaria use the bargain Bavarian Pass that gives you unlimited use of regional trains and buses and city transports all over Bavaria for a day for about 30-35 euros. Other good rail sites: www.seat61.com; BETS-European Rail Experts and www.ricksteves.com.

I may suggest doing day trip or overnight to Salzburg from Munich and then say base in lovely Garmisch-Partenkirchen to see Oberammaergau, Fussen, etc.

Then go straight to Interlaken as fast as possible - book those tickets far in advance to get discounted fares at: www.bahn.de/en. In Interlaken area seems not doing enough on public transit to warrant any pass or Half-Fare Card, etc. Just buy Germany/Austria to Murren ticket at www.bahn.de/en again for discounted fares. Murren-zurich just buy at station day of travel. www.sbb.ch is Swiss Railways site.

How far in advance can you book? The site doesn't seem to work for me for my date in August yet, but I also tried a closer date in April and it did not work. Perhaps this has to do with the itinerary.

Also, do you know how large Zurich station is? The itinerary allows only 12 minutes to transfer from platform 9 to 32 in Zurich.

Think it is usually 90 dys or so out. www.bahn.de/en only books trains involving Germany. Why not April?

What exact tickets were you trying to book? and what site?

At Both, Salzburg and Fuessen, you are close to many glaciers and alpine hiking trails.
You waste your time with a 8 hrs train ride up to Lauterbrunnen in ordr to see more or less the same.

In a bit more than 1 week, I would visit either Bavarian/Austrian castles, museums and mountains or
Swiss castles, museums and mountains

If you have booked home flight from Zurich then the Jungfrau Region and Wengen and Murren would be best for your Alpine experience. If not consider neckervd's advice. But it is a long 8 hr train ride from Fussen or 6 hr one from Innsbruck to Interlaken-Ost - Wengen or Murren being an hour or so longer.

Can you base yourself out of Salzburg for the hiking you mentioned in Austria?

Or, is there somewhere else that has the best hiking in Austria, such as a place to stay in the mountains?

I think neckervd is onto such places between Innsbruck region and farther west - like famous Alpine resorts like St Anton and Kitgzbuhel - or ones to east of Salzburg like Hallstatt but I think there are few that would be a short commute from Salzburg. Neckervd is always right on and she/he/it will come back to respond I'm sure.

I'll leave it to others to address your time in the mountains. Given what you said of your interests, and assuming any chance of jet lag, I think plan B makes better sense for Bavaria, so you have 2.5 days in Munich. JMO.

Ok, thanks everyone. Based on feedback here I decided there is not enough time to go to Salzburg on this trip and to stay in Munich for 3 nights rather than 2 nights.

I will keep the lauterbrunnen portion of the trip, at least for now that is my plan, since I am flying out of Zurich.

Is the train from Fuessen to Zurich etc. any more or less scenic than the train from Innsbruck?

Yes Fussen - Zurich not that scenic (though this whole area most would consider to be scenic) and Innsbruck to Swiss border area very scenic at times but not as scenic as you'll see in Interlaken area.

The really scenic mountain vallleys and glaciers are south of the Innsbruck - Zurich railway line. From the train you will see nothing of all that. But I know that people from overseas are not interested in the Austiran Alps (may be because everything there is much cheaper than in Switzerland) nor in the alpine approach from Austria to Switzerland (Engadin Valley).

In order to answer your questions: the mountains along the Innsbruck - Zurich line are a bit higher and you will see more cliffs than on the Ulrichsbruecke-Fuessen - Kempten - Zurich line which goes rather through midlands.
The direct Zurich - Bern - Interlaken line too doesn't really go through the Alps.

Austrian Alps often overlooked... no debate but is there an area comparable to say Jungfrau Region around Interlaken with the awesome views (no doubt) and the myriad of mountain trains and aerial gondolas going off in all directions, making it so easy for folks to spend several days there seeing very varied things - even boat rides on two lakes bookending Interlaken? Been to Kitzbuhel and did not see such a panoply of transports but maybe some place?