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I don't think there is any reason why you shouldn't start your visit in Venice and come to Milan later on. I suppose your explanation about flights is sound and reasonable, although there are plenty of flights to Venezia Tessera as well as to Verona airport.
Normally, Milano is not considered worth visiting for more than one day, although there are monuments and museums here as well. If you can spare 10-15 days to visit Northern Italy, then you should be able to have at least a couple of days in Milan (a bit on the expensive side as far as hotels are concerned...), at least 4 in Verona if you plan to visit Lake Garda as well, then the rest for Venezia, but you shouldn't miss Padua and the Brenta Riviera with the various Palladio villas, Treviso and perhaps Asolo or Bassano del Grappa.
"Acqua alta" may be a problem, but it is not all that frequent in early November, and quite often the weather is still pleasant. Enjoy your visit, whichever direction you will travel.