Some Fenders I've seen in shops usually have to have their necks shoved over to align them. The screws need to be loosened slightly then the neck can be set left or right by grabbing it and torquing it as required. This usually does the trick. Some nuts are also cut bad and the strings won't line up with the fret markers. A new nut replacement fixes that. I realize that you expected better quality and was disapointed in the guitar. I too am really picky about stuff like that but after straightening out 2 necks on 2 Fenders and replacing 2 nuts I am no longer afraid of those kinds of problems. Any guitar can be fixed.
Guitars/Bass - MIM Fender Classic 50s Strat, MIM Fender Standard Strat, Squier Classic Vibe 50s Tele, Gibson Les Paul Studio, Epi '56 Gold Top Les Paul, Martin DSR acoustic, Sigma Martin Auditorium electric/acoustic, Squier Jazz Bass.
Amps/Cabinets/Modelers - Model 2558 50 watt Marshall Silver Anniversary Jubilee combo w/ Celestion Vintage 30s, 4x12 Marshall cabinet w/25 watt Greenback Celestions, Fender Blues Junior w/ a couple of Billm mods, Line 6 POD 2.0, Roland Micro Cube
Pedals/Effects - Cry Baby Classic Wah, Boss TU-2, Boss NS-2, Boss RC-2 Loop Station, Ross Compressor, MXR Micro Amp, Danelectro FAB Echo, Danelectro FAB Chorus, Danelectro Chicken Salad, Marshall Guv'nor Plus, Marshall Echohead, Duhvoodooman's Zonkin' Yellow Screamer, Digitech Digiverb, Digitech Bad Monkey, Dunlop Fuzz Face, Homemade Loop Bypass pedal, Duhvoodooman's Sonic Tonic (Maxon SD-9 clone +), Voodoo Labs Superfuzz