Hmm, I see what you mean, Bernard, and looks like Richard's in agreement too. OK, I'll think seriously about that then - it's stuff like that from "power users" that's good to pick up. Extra assembly time will be a pain, but if it's something that'll definitely give some benefit then it's worth adding it to the list. Re my mate from Tektronix, returns under warranty were his big problem, but they had maintenance contracts as well - still, I guess it's likely that you're right and most of the problems came down to manufacturing problems revealing themselves sooner or later.
Transformer-wise, yes, the transformer will be right at the back of the box. All the interesting bits will be happening at the front, as close to the inputs as possible.
For instruments, I was kind of expecting people to be using a separate DI box. But if you reckon people are likely to want to jack instruments in directly, maybe a hi-Z option is worth it then. That'll mean axing a low-impedance option though (500R, say, per Anahata's suggestion) but it doesn't sound like that's a major priority. I've only really got room for one extra pushbutton switch - there isn't space to add a pot or a big old three-position slide switch - so it's whatever gets the most value from that pushbutton.
Like Bernard says, it's the old story - everyone wants different things. Ask two people and get three opinions... ;-)