Having several MIJ, MIA and MIMs to compare, I'd say the Mexican plant is not especially precise, the body radius is inconsistent, the finish isn't quite as flat and even, but then again, they're still very good and they look and feel hand made, and that's nice. I think it was Jimmy Vaughan who said he thought modern MIMs were more like vintage Fenders in terms of build quality, I could believe that. The MIJ's are so uniform that you'd swear the whole thing is made by robots start to end, you have to have different frames of mind to appreciate a guitar for being either too perfect, or somewhat imperfect.
Regarding the wood, I've never seen an substantial reason to believe the wood is somehow substandard, either in terms of tone or looks or durability. Decent wood is not hard to come by, why should we believe they're having to settle for ply wood or pine? They are at a high enough price point that such concessions shouldn't be necessary.