USA made Fender is the popular choice for the reason that Fender originated in the States. Like people will choose a Japan made Boss pedal over one made in Taiwan. Or a German manufactured BMW over ones assembled by American General Motors. It's a sensible mindset.
But being a non-conformist, I digress from popular choices. I prefer MIJ's because, I don't know, it's different? Cult status, perhaps? Also, I like the feel of the neck better. My only gripe is the inferior electronics, which is easily replaceable anyway. At some respect I disagree with the resale issue. I bought a used MIJ Tele for $530. Sold it after a year for $600. Somebody is offering me $750 for my 72 Telecaster Custom. That's way more than what I've actually paid for. The MIJ 52 Tele Reissue sells for around $1000 to $1200 in England.
On the other hand, I'd prefer a Gibson over any Japanese copy Les Paul.