I've gone through a lot of Strat phases, but playing vintage and custom shops have really changed my perspective though. I've come to really appreciate the deep body contours of 50s Strats and the texture of the nitro finish; 54-57 chunky neck profiles, Callaham does great improvements to the fender bridge saddles and saddles. I'm intrigued by roasted maple necks, one piece and rosewood top; I'm more on the fence about quarter-sawn due to the nature of it actually being too stiff which can make the truss rod less effective and can warp in a twist which is unfixable if it warps. Not much has really been improved in stratocasters since the early 60s. the 11-hole pick guard was an improvement for sure.
Now in terms of a modern Strat build, I'd be going along these lines:
Roasted Maple CBS Head Neck with *adjustment at the top rather than bottom*, 56 boat profile, Stainless Steel 6230 Fret, black dot for maple/abalone dot inlays for rosewood, 7.25" radius preferably, but 9.5 is fine. Nitro finish (I've never had an issue bending out on a 7.25 radius neck, not sure what issue people are having with bending)
Roasted Ash 50s deep contour body with nitro finish that shows off the grain
Callaham Vintage Hardware Kit
schaller strap locks
Mojotone '59 single coil set and electronics, .1uf capacitors on the tone pots, 250k fender tone saver (cap/resistor, but they look cool in the fender tone saver form)
My baby is a masterbuilt 54 strat that I've modded the electronics a bit -- they haven't really improved much since 1954