In 5 years, you'll be happier with your choice if you focus on the house, the neighborhood and amenities than who you purchased the home from. Short sales can take 6-9 months or even more. During that period other homes will enter the market and be purchased by other buyers.
Getting a good deal is important, but getting a house you love is more important. If you fall in love with a short sale, and are willing to commit the time, frustration and uncertainty while you wait for a banks response, get what you love. If the home is Bank owned, investor owned or private party owned have the best available agent negotiate the best deal possible and enjoy your home.
If you are strictly looking at investment property for use as a rental or flipping, pay more attention to location and overall desirability for tenants or resale. Auctions would be your best bet, but only if you are able to pay cash and know the market. Best of luck with your purchase.