Fender Starcaster. The original, semi-hollow archtop one, not the current cheap Strat.
25" scale necks for 6-string guitars and 26", 26.5" or 27" for 7-strings.
More 7-string bodies, certainly. Anything would do, even just a more standard super-Strat than the weird, melted-looking one that is currently available.
More chambered and semi-hollow designs. I think this would be a no-brainer for any body style where lam tops are an option.
The Strat/Thinline Tele hybrid that Fender's Japanese division put out a few years ago. USACG offer it as a standard body style, but being in the UK, it's hard to order from them!
Vintage modern neck construction for more headstock shapes, especially conversion scale and tiltback necks. I can't stand the 'pro' construction, to put it simply.
Generally more bridge/pickup/neck contour options. To be blunt about it, every other company similar to Warmoth offers more hardware, electronic and profile options and with fewer upcharges, but Warmoth is the one with the fancy, easy-to-order website. I've said it before and I'll say it again, I would buy twice as many Warmoth products if there were simply things like ToM and stopbars available on Jaguar bodies, EMG routes for 7-strings, etc.
But, most of all, I'd love a Sambora (ESP LTD SA-2) body style. Of course, it'll never happen. It's trademarked to buggery, I'd bet, and it's massively unpopular. But I'd love it.