I have some experience with MIM Strats as I own 1996 HSS in Crimson Red sparkle, a 2001 SSS in Brown sunburst and a 2003 Classic 50s in Daphne blue finish.
the guitars were chosen for superior feel and playability, and all were good deals financially. i could not say that one is of higher quality than the others. In all truth, I think I prefer the 1996 model the best. it has a smooth soft V neck and sounds great. they all FEEL very different, and timbre is different from one to another. Overall build quality I would say is equal from 1996 thru 2003. Then again, I passed on a bunch of MIM Strats in the past that did not meet my high standards, and were less than stellar examples, so my experience is skewed by my picking what I consider "prime examples" of their vintages.
I buy what I like, and I own MIA, MIJ, MIM Strats. All different, all good, all fun to play, all sound like Strats, or at least close.