I enjoyed Lyon a lot in 2017. It has many sights, and it's known for great food. (It helps if you like innards.) The town of Annecy is about 2 hours from Lyon by train, and Lyon is large enough that you'd probably need to add a non-negligible amount of time to get from your lodgings to Lyon Part Dieu station. Therefore, if you're thinking of Annecy as the likely destination on the lake, I'd say it's quite far away for a day trip. On the other hand, the historic center of Annecy is relatively small and doesn't take a great deal of time to see. It might come down to whether you want to take boat trip on the lake (assuming availability in the fall) and/or a bike ride around the lake. I found Old Town Annecy very full of tourists during summer day-tripping hours but would guess that wouldn't be much of a problem in Oct/Nov unless you hit the town on a weekend day with fabulous weather.
I suspect it would take even longer to get to smaller lake towns/villages from Lyon by public transportation, but I do not know for sure.
There's a (non-express) rail line running along the Riviera that makes hopping from one coastal town to another very simple. Inland destinations generally require used of buses, and Nice is sort of the bus hub, so it's very helpful to make a list of your must-visit destinations and maybe-visit destinations before choosing a base in the area. If they're all on the coast, you won't waste too much time by choosing a somewhat-off-center base. However, the trains aren't particularly fast, so if I had a lot of side trips planned, I'd take a good look at the map and try to choose a sort-of-centrally-located base.
You can investigate travel times by train on the SNCF Connect website:
SNCF Connect
I haven't researched weather in France for October or November. When I'm considering a shoulder-season or off-season trip, I look at the actual, historical, day-by-day weather statistics available on the timeanddate.com website. I want to know how chilly it could get as well as how hot (to decide whether I must have an air-conditioned room). I've learned to pay attention to more than just the high temperature for the day, because I may not see that temperature until noon. I'd recommend comparing historical weather in Lyon, Annecy and Nice to see whether there's enough variation that you need to consider the difference, given your personal weather preferences.
Lyon weather -- November 2023
That looks less-than-ideal to me, but you may be more interested in avoiding heat than I am. Use the pull-down box at the right, just above the graph, to change the month and year displayed. I check the critical month(s) for the most recent five years because there can be a great deal of year-to-year variation. Use the Search box at the upper right to change the location.
Rain, especially in cool weather, can affect sightseeing comfort, so I'd also look at the monthly-average statistics to be found in the climate-summary chart appearing in the Wikipedia entry for potential destination cities. Here's Lyon:
Wikipedia -- Lyon << Scroll down and look for the colorful chart.
I usually really enjoy less touristy cities, but I was somewhat disappointed by Marseille in 2017. Although it has some points of interest, the museums were far less interesting to me than those in Lyon and Nice. I'm more interested in art than in history, and I may have caught the new MUCEM before all of its exhibitions were open; all I remember was something about garbage/recycling that seemed mostly designed for children.
I don't know how early in the fall the mistral becomes a potential risk. Be aware that the days will be a lot shorter in November than in October. See the Wikipedia chart.
