Switzerland for 3 days in September

Does the flight get in very later or do you have another reason for staying in Geneva? With your limited time, going straight to the mountains gives you the best shot at completing all you want to do there. Travel time to Gimmelwald is just under 4 hours. If you're also returning via Geneva, any sightseeing there might be done later, when you know how the mountain part went.

Yes, mountain weather often changes through the day, with early morning sometimes being the clearest, as well as the Schilthorn and Jungfraujoch rides have discounts on the first couple of morning departures. In less ideal weather, you could still enjoy a valley walk, beer hall, or Rick's poor-weather recommendation for the Ballenberg Open-Air Museum.

Reliable weather predictions are difficult more than maybe 3 days out unless a low has sat down and isn't moving. This doesn't stop the usual online weather sites (computer generated) from trying to estimate what it will be like in 10days time. By late September a fine dry day can begin with early morning mist.

Generally in Switzerland weather fronts on an otherwise stable day can be in and gone within hours but low pressure systems with poor weather can hang on for over a week (I know, I've wasted weeks!).

My big question is Gimmelwald. Why? Are you sure? I see it mentioned a lot on this forum and often wonder. It's not even big enough to be called a village. I know it has views and hiking but so does the rest of the Swiss Alps. It takes nearly 4 hours to reach from Geneva (using 3 trains, a bus and the cable car).

Which brings us to your obvious worry, cloud cover. If a week long low pressure sat down on the area it could be like being in fog and the only way out is the cable car.

the flight does get in pretty late and Geneva is kind of just the base to spend the night before heading out in the morning.

As for staying in Gimmelwald, I want to lodge there because I love the quaint little village feel. I realize there isn't actually a lot there but I am planning on spending any time not hiking more in the valley rather than trying to find something to do in gimmelwald.

For predicting the weather, I like using Meteo Swiss:
http://www.meteoswiss.admin.ch/home.html?tab=overview
The weather in that gorgeous mountainous area is so volatile, though, that I don't think any source is reliable until a day or two before, and preferably the night before, or the morning of!
The views are still spectacular, even with haze and clouds, as long as it isn't socked in with a thick dense blanket of clouds, clinging to the entire mountain for the whole day. I hope you get good enough weather to enjoy the beautiful view, even if only the lower half of the mountains are visible, but it's wise of you to ask about back up plans, just in case.

Viewless suggestions in the Jungfrau region:

Trummelbach Falls, in Lauterbrunnen Valley, below Gimmelwald--The waterfalls are INSIDE a mountain, and drain the glaciers above. Take the cable car down from Gimmelwald to the Stechelberg station; then take the bus from there to the Trummelbach Falls stop (going in the direction of Lauterbrunnen). Or you can walk in the valley towards Lauterbrunnen and enjoy the cliffs and waterfalls that are close-up.

Allmendhubel--It's the place that is up a funicular from Mürren, which is one cable car stop above Gimmelwald.
It has spectacular views of itself right there, with huge green glacier bowls of meadows and mountain. By the way, Mürren is a very cute town, itself, with old wooden chalets with blooming flowers in their window boxes and gardens.

Take the Lake Thun or Lake Brienz ship from Interlaken, and enjoy the blue-green water. To get there, take the train from Lauterbrunnen to Interlaken Ost for Lake Brienz (Brienzersee) (bright blue-green water), or to Interlaken West for Lake Thun (Thunersee) (bright blue water). The medieval town of Thun has a 12th century castle you can walk through.

Giessbach Falls on Lake Brienz--It's a gorgeous set of waterfalls with a path to go over and behind the falls. The path starts at the Giessbach Hotel, which you get to from the Lake Brienz ship. (Take a train from Interlaken Ost to Brienz, and a ship from Brienz across to Giessbach; then a funicular up from there to the hotel. The hotel has a nice outdoor cafe terrace and a snack bar, open through lunch time.)

Aareschlucht (Aare River Gorge)--It's a dramatic canyon gorge with a cliff walk over the rushing river below. To get there, take the train from Lauterbrunnen to Interlaken Ost; change to the train toward Luzern (the one that goes via BRUNIG), and switch trains at the Meiringen stop to a little train towards Innertkirchen. When it's going through a tunnel, there's a push-button "on request" stop (auf verlangen) for the Aareschlucht Ost (east entrance). You'll come out the door of the mountain tunnel to a suspension walking bridge, go across the bridge, walk up the other side to the entrance to the gorge cliff walk. The walk is maybe a little over a mile long, then there's another (open air) train station past the souvenir shop. You can take the train back to Meiringen, or walk there. --Meiringen's a cute town, itself. The famous Reichenbach Falls, from the Sherlock Holmes story is there, as well as a Sherlock Holmes museum. Meiringen has huge cliffs around it with loads of other waterfalls--biggest after heavy rains.

Thank you so much!! those ideas all sound amazing! I might have to check out some of those regardless of if we can hike