In reply to ianstevens:
I don't know it in Autumn but I'd have though Chamonix would suit very well. I've done summer holiday there last few years (staying in Montroc which is a quiet spek just up valley from Argentier). If flights to Geneva make sense for you it is then very easy to get to Cham via bus or airport transfer like Alpybus/Mountain Transfers and others of that type.
Once there transport around the valley is easy with local buses and the train.... the tourist tax that you pay if staying in formal accommodation (and possibly camp sites too) entitles you to some kind of card that gets you on buses for free but you generally need to ask for it as the venues tend not to hand them out unless asked.
I'd be surprised if some of the main and most touristy lifts were still not running to get you up high and the train up Mer deGlace and from St Gervais up will presumably still run. Use these or foot power to get high and worlds your oyster. Both sides of valley have a good network of valley paths and tracks and both sides have a higher level traverse at around 2,000 meters altitude which should be OK as I assume snow may not be that low yet. And also higher stuff clearly... but the classic traverse of the valley is at about 2,000 or so. You could run up valley and up Le Tour and drop down to Vallorcine and get train back, do a traverse of the Grande Balcone North and or South depending on energy levels. There is a web site that has maps and instructions for assorted runs in short/medium and long lengths. Just google Chamonix valley trail running and you should find it.
If you are familiar with your speed at altitude fine, but for ref (admittedly in summer heat) I was a lot slower at 2 to 2,500 than normal, even reasonably acclimatised. Ran from Col des Montets up to Lac Blanc, then on to Brevant above Cham via Le Index then back to Argentier on lower tracks and admittedly taking it easy and having a lunch stop etc the 13 odd miles of that took me about 5 hours.... pitiful compared with my UK speed over similar distance and height gains.... If doing that you have a choice of going high straight away on path up into the aguilles rouge, or staying a bit lower and heading to Petite Aguillettes Argentier from where the path goes up on ladders and a few walkways etc for a bit.
If using lifts (assuming they are open) there are good deals on multi day passes that might make sense, cheapest type (still expensive) is consecutive days, or you can pay a fraction more for non consecutive. Covers the lifts and the mountain railways.
Enjoy.