I wouldn't regard the Stansted Express as the gold standard of airport express trains. When I was in Liverpool station last, for example, it had been replaced with bus service allegedly because of bad weather, although all other trains were running normally.

Also don't assume that because the Malpensa express is scheduled for 40 minutes and runs every 30 minutes that it will adhere to either of those -- sure didn't for me, and I wasn't there at busy times at all.

However, both Stansted and Malpensa are havens for LCCs, so if that is your preference, you'll probably end up there.