I don't really think Harper's negatives are higher than Machado's, if such negatives even exist. They both have the potential to get ripped on WIP as being primadonnas or bad in the clubhouse (of course, anybody does, by that standard). It's just that Manny got all the attention this past season (in part because he was in the World Series).
The reasons to prefer Manny, for me, are the same as ever: no draft pick compensation and more positional value (and more positional value for longer, Harper's headed for 1B). Plus the Phillies have more acceptable OF options - some combination of Herrera, Quinn and Williams in RF sounds better to me than Franco, and if they go external it is cheaper/easier to get a 4th OF than a new 3B.
Both would certainly be fun, I have trouble believing the market has collapsed to that extent. Nightengale (who's certainly not infallible) flat-out said Harper to Phils and Machado to White Sox, we shall see. As far as agents planting stories, be interesting to see what Heyman tweets about Harper (he has also tweeted there's a third team in on Manny).