I have a wishlist and a new case project in mind myself, as I hate the Escom/Quikpak case design. Not all of my ideals are compatible with your 3 requirements, but here's my ideas anyway...
I hate how the "lid" of the Escom/Quikpak case fits onto the frame. The side comes off, but wraps around the top and bottom , so to open it up you can't leave it standing, you have to lay it on its side. Don't do anything so awkward as that, I want easy to open, easy to poke around in, all without having to flip it over or unplug anything or whatever.
Don't put anything in the way of decent heatsink/fan units. I had to cut part of one of the center brackets to make room to put a small 40mm fan on my 060 when I overclocked it. I couldn't mind having room for a bigger fan just to reduce the noise a bit, as them 40mm things get nasty at times.
Try to make sure that users of cybervision-PPC, SCSI modules for CSMK2, etc. will have room for their toys. Including both orientation versions of the CVPPC, as I understand there were two possibilities there. Also for potentially oversized cards, I understand some 060 cards were much bigger than the "standard" CPU module.
Now, for something I'd like to do in my own case project, is a 90-degree zorro slot adaptor, so I can for my prometheus into the "bottom" Zorro slot, and have it point further "down"/away from CPU. As Prometheus would otherwise block all my Zorro slots, and it won't fit in the top Zorro slot as PCI cards would conflict with the SCSI/AV risers, I'd like to make new space to allow PCI cards and Zorro cards to co-exist. This would create some empty space on the left end of your case which you probably don't want to do. If I ever get around to working on my own project, it'll be a tower with extra space inthe bottom for the Prometheus to poke down into, out of the way of whatever Zorro cards or Video Toaster that I'd like to keep installed.
I hate drive rails. My A4000T only came with one set so I had to order more, they get lost, and are just annoying. Just put screw holes in the drive cage so life is less hassle.
Whatever the front panel is made of, try to get things to complement the colors that CDROM drives and stuff come in. I wouldn't want a case that looks very cool on its own, but no drives match it and it ends up looking stupid.
I believe the A4000T motherboard is one of the larger in the AT standard formats. For kicks, see if you can get things sorted out to also allow ATX, Mini-ITX or Flex-ATX boards as well, so AmigaOne XE, Micro or Troika boards could potentially go in there as well. This could get awkward and might not be reasonable, but is something to think about.
See if you can figure out something to make a convenient external floppy port. I believe there is a place on one of the rear riser cards to solder a floppy connector, it's just not there and I don't thing there is a hole in the Escom/Quikpak case for it. But as some people have had trouble with their floppies dieing, and they may have external drives for older Amigas laying around, it might be a convenience to be appreciated compared to tracking down a compatible replacement internal drive.