Aluminum windows with a flange behind siding/brick/trim should be removed completely if possible. My first choice would be to install a good window sized to fit the same opening and use a nailing fin to install. Back caulk the nailing fin, insulate, tape over the fin and use flashing in accordance with current new construction guidelines.

Don't settle for a "snap-on nail fin" or something screwed on to make an easy installation. Custom size windows with nailing fins are readily available from quality suppliers.

There is no one simple rule to replacing windows. The only rule to follow is do it correctly regardless of how much extra time it takes vs. the quickest or easiest way. Choose your advice on products and choose your installer using this rule and you will be happy with the end result.