You know.....
The real answer to this question has more to do with what youre looking for and how picky you are than anything else and that has to do with quality and what "qualities" youre sensitive to.
There are definate differences between the MIMs amd the MIAs and once again, it really comes down to quality. If you remove a MIM trem system and compare it side-by-side with the MIA, the differenses are obvious and the MIA wins hands down. Now, compare the MIA or Fender Vintage trem to a Callaham Trem and you'll find more obvious differences, all related to QUAILTY. Same with the bodys. The MIA uses fewer pcs to build the body and usually, the higher end bodies have even fewer pcs and therefore, more ring.
Necks? We can write a book about necks but for tone, the bigger the better. Feel comes from the neck shape and how the edges are shaped and/or rolled. More $$$ buys moreshop time and a better neck.
In a nutshell, what the MIAs start to do is give the player a higher quality, better playing instrument, at a price that might be affordable.
Heres what I've found...
I have a MIM that I've set up very carefully and I've installed some expensive pickups in it as well. It plays and sounds damn good and everyone who play it is happy and admiring of it untill they take a spin on the EJ Sig. They might like the MIM a lot but give em a choice and they'll take the EJ, hands down. It not only sounds better plugged or unplugged but it plays and feels better. Much better.
What you like and need, usually changes with time, experience and circumstances. Therefore, these are fruitless discussions. (Hell... My 13yo Grandson thinks his Starcaster is the bees knees!) unless the discussion takes place between people who have some similar experiences and a matching understanding of the different levels of quality.
Just remember... SRV's instruments were all rebuilt several times by a master luthier and theres a reason why most good players buy hand rebuilt or custom guitars and it aint ego. They really are better guitars!