To make a comparison with the US, Linate is the equivalent of Washinghton Reagan National, Malpensa is Dulles.
LIN can't have intercontinental flights, because the runway is only 8000ft. In order to develop MXP flights from LIN are limited to the EU capitals and major hubs. There are also noise restrictions due to the proximity to the city. The airport closes at night, and there can be only a limited number of flights hourly.
Linate is the City airport that is preferred by business travelers because of its proximity. Most intra Europe flights with traditional airlines are from LIN. For example I don't think you can fly to CDG from MXP anymore. AirFrance uses only LIN. It is also the preferred airport by major carriers, because it's the more lucrative (business travelers pay more). I've used both, and both are easy to use. LIN is certainly preferable if you are in Milan. It's only 8km (5miles) from the Duomo, rather than over 50km of MXP, The taxi (or bus) can get you there in 15 min and the cost is obviously less. But check the prices of airfare. LIN might cost a bit more.
If you want to stay in Stresa, MXP is better. However one night in Stresa only is not worth the trouble. If you don't have a car, getting from Stresa to MXP requires a train to Gallarate (for two people 10 euro for 35 min) then a taxi (35 euro for 10 min). There is also a bus with SAFduemila, but it has limited runs. Arona is also on the lake, but closer to Gallarate. Both train and bus stop there too.