two weeks in Switzerland in September

PHJ I often suggest to people who want to really experience Switzerland is to spend some time in the German-speaking part, and some in the French-speaking part. So I would suggest the Lake Geneva area for your second place - Lausanne or Montreux, or some smaller city like Sion. Geneva is fine too - I think nicer than Zurich. Squeeze in the Italian part too, if you have time.

If you want to see spectacular mountains the the Berner Oberland will not disappoint. Lots of walking and hiking and cable cars. The previous poster mentioned Sion in Valais and that is also a nice base for hiking. It's right on the main train line that connects all the towns of Valais down and around to Lake Geneva. To the north, you can go up to the Rhone Glacier by cogwheel train. If you want to be adventuresome, you can also get to places like the Sanetsch Glacier (infrequent bus service but one of the most spectacular, remote hikes I've done in Europe), and the St. Bernard Pass where the famous dogs were first bred - they still breed them there and you can visit them. The town of Sion itself is nestled in a valley that is quilted with vineyards. The town is lovely; two hills in the center, one topped with a ruined castle and the other topped by an ancient church. From Sion you can easily get to Zermatt to see the Matterhorn and hike, take a gondola up to Mont Fort, one of the highest peaks in the area, and quite a few glaciers that are in the mountains around the valley. With the exception of Zermatt, if you want to hike you'll need to navigate the bus system in the area but it's easy to do and well worth the effort. Outside of Zermatt, the other tourists in and around Valais are mainly Europeans on holiday. The northeastern end of the valley speaks a version of German. From just north of Sion and southwest they speak French.

Grindelwald would be my preference in the winter because it has the best skiing in the Berner Oberland, but Mürren is a good choice for late summer.

"Please don't get me started on skiing here....lol"

Sorry, Chris, but I have to react to that. Based on your recommendations on this website, I went out of my way to try out the slopes around Mürren. Let's just call it the most disappointing day of skiing I've experienced in the Alps. Yes, Mürren is beautiful, but the skiing just wasn't that good. No where near as good as the slopes on the Wengen-Grindelwald side. Not even close.

With respect to your question about finding holiday apartments to rent outside the Saturday to Saturday window. We have never had a problem finding an apartment in Switzerland for 4-5 nights. A lot of apartment owners will be flexible, so it never hurts to ask. Occasionally we have been asked to pay a slight premium to make up for the fact that they may not get the full week rental but it has never been outrageous.

We stayed in Lauterbrunnen for 4 nights and loved it. We could catch the train and cable cars right out our front door practically. There were many walking paths right there as well. It was absolutely amazing!!!

Thanks for the replies. For a second base, Valais looks beautiful. Which would be a better town to be in, Sion or Zermatt? In addition to easy access to hikes, we'd like to be in a town with good walking and things to see in case the weather is bad.
From the other posts I've read, since we're heading to Venice by train, Brig is the station we'll need. Is that correct?
This is our first trip to Switzerland and we're very excited to go. Many thanks to all.

If budget is an issue then Zermatt will break the bank. It is expensive even by Swiss standards which is saying something. If you do have the money then you should stay there if you want to hike directly out of town.
If you do end up with a rainy day then Zermatt would have more to do in town. Sion is really beautiful but, if it rains, there might not be as much to do. The core part of town is the medieval shopping area and another more modern shopping area adjacent to it. Hiking directly out of Sion would be up through the vineyards unless you take a bus out of town up into the hills.
Zermatt has a much larger central town shopping street and alpine hiking is right there if you take a gondola up out of town for 10 minutes. Everything is set up for tourists but the town is very picturesque. Sion is more of a "real" Swiss town where people live and work - there are tourists but most people walking around are the locals.
Another thing that most people don't know about in the area are the bisses; ancient, hand-dug water channels that were designed to bring water from the high alps down to the vineyards and orchards in Valais. Some of them are 600 - 700 years old. They surround the entire valley and they all have trails that follow them, some with spectacular views. Here's a website about them that gives more info...
Valais Bisses