Alps: French and Swiss or Bavarian and Austrian?

Repost from /r/travel, but looking for help wherever I can get it.

Looking for some help/feedback with honeymoon plans to the Alps region. We are torn between doing a combination of the French and Swiss Alps or Bavarian and Austrian. We have already been to the Dolomites so while we considered the Italian Alps, we would like to go to a region where neither of us have gone before. We are going later October/early November for 12 days (could do 13) with a budget of around 6,000 euro and will be traveling from Ireland. Hoping to do either itinerary by public transport rather than renting a car.

What we are looking for:

Hoping to see some autumn colours and get some hiking in, ideally at least one hike at each, but some stops we would double up. We know the weather can be hit or miss at this time in both regions which we are okay with, but if anyone has more input about where it might be slightly more predictable in the region or one itinerary over the other where hiking would be better, this would influence our decision. The two of us have hiked and traveled all over the world (Nepal, South America, New Zealand, Australia, USA) so have a good amount of experience both in the hiking and travel departments. We like small cities or towns over big cities, especially for the honeymoon where we will be trying to relax and enjoy each other's company for the most part. One must of the honeymoon other than hiking is that there is one stop ideally at the start where we would be able to stay some where particularly luxurious and just decompress on the premises in a spa and the surrounding area.

Here are the two itineraries we are considering right now:

French/Swiss:

Fly into Geneva

Days 1-4: Chamonix

Days 4-6: Megev (this would mostly be to go to Flocons de Sel as we are big foodies)

Days 6-9: Zermatt

Days 9-12: Grindelwald/Interlaken (hotel we are interested in currently is in Grindelwald)

Fly back out of Geneva

Pros of this itinerary:

• Outstanding scenery and hiking if the weather is good.
• Outstanding food at reasonable prices on the French side.
• Easy transport by trains.
• 3 star Michelin restaurant at an extraordinarily good price.

Cons:

• Switzerland be expensive.
• Have read conflicting things about Zermatt and Interlaken being very touristy (though it will be quiet this time of the year).
• It might be too quiet with restaurants being closed etc. due to seasonality. It's hard to get a read on the extent of this by location. We have at least found hotels we would be happy with in each place that are definitely open.

Bavarian/Austrian:

Fly into Munich

Days 1-4 : Garmisch-Partenkirchen

Days 4-7: Innsbruck

Days 7-10: Kitzbühel

Days 10-12: Tegernsee

Fly back out of Munich

Pros:

• Much cheaper than the first itinerary – this means we'd be able to stretch the budget more with nicer hotels, food, etc..
• Seems like some of these places might have better weather (I could be wrong on this?) also means hiking might be easier.
• Some of the hotels in addition to being cheaper, have a half board option which is appealing in the event of restaurants closing for seasonality in the smaller towns.

Cons

• Still very nice scenery here, but not as dramatic as the first itinerary.
• Not quite as well connected by transport at least for last part of itinerary – could be fixed by changing those stops though.

Also looked at Zell Am See, Zell am Ziller, and Seefeld. One of the above stops would only be two nights, but not decided on which.

I have done more research on the former and had some recommendations from friends who have traveled in the area. For the Bavarian/Austrian itinerary I have done a good bit of research as well, but from what I can tell there are lots of smaller towns people tend to recommend and less obvious big must see places like Zermatt and Interlaken. A good problem in our eyes, but also has made it hard to decide where to go. Would like to keep either itinerary to a max of 4 locations and would be even better to only go to 3.

Any help, recommendations or critiques welcome! I will admit I haven't explored every angle of the above so if there's something glaringly obvious please feel free to point out. Thanks for any feedback.