In terms of facilities, it's a choice between a 15 minute taxi ride for EUR12-15 (Linate), a 30 minute bus ride (EUR1.50), als to Linate or a 40-50 minute train ride (around EUR8 IIRC), to Malpensa.

Malpensa is a bigger, newer airport, but I never use it unless I have to because I usually want to go to Milan city centre.

Linate is older, with mostly bus gates, but the sheer convenience wins every time,

I realise that there was a very unfortunate SK crash there a couple of years ago, and that the fault for this may lie in part with Linate ground control, but I would not let that influence my choice of Milan airport (put bluntly, LIN and MXP are run by the same company, and I would be amazed if their respective ground contollers are not trained by the same organisation). For the record, I have never felt unsafe using wither airport.