I generally try to find simplicity in travel, avoiding multiple changes wherever possible.
So looking at the direct trains, Como indeed did look like a practical choice, but as that's a no on its own merits, then I'd be looking at options based on changing at Como, or Milano / changing at Milano.
At that time of year I'd typically lean into cities, as there's less daylight to explore the countryside, and cities give stuff to enjoy in the evening, as well as the day.
Options from a quick look at the map:
- Varese, changing at Como (just under an hour from Como by public transport)... but I don't know it, and what looks appealing to me would be the local parks, hence might be better in Sept/Oct and with a car
- Novara, changing at Milano (train or bus) a charming and under-touristed city. Some good wine regions nearby (Ghemme, Gattinara, etc.), plus in an area where the risotto is excellent. Vercelli offers an easy day trip as well, along with slightly longer options to Ivrea, Biella and Torino (plus Milano itself)