1) Make it a bit taller, the case can't fit todays big GPUs like Zotac GTX1080Ti (12.8'') the FT05 has a max PCI cards of 12.3'', doesn't need much, probably around 13'' PCI cards clearance would be enough.
2) By making it taller will also help the PSU slot, while i like a lot the position of the HDD cage, i only use half with a single 3.5, the space on the side is shared with the PSU, that means the hdd cage limits the size of PSU you can install, we are at an era that all is more efficient, but seems newer psu tiatnium are bigger, take into account Seasonics 650W Titanitum are 170mm and EVGA (superflower) 750W Titanium are 180mm, atm i cant move toward either because there is not enough room with the modular cables, it really doesn't need that much, as 160mm PSU work fine with the hdd installed, so its an inch or inch and half to have room for the newer tendency of PSU, and this is without considering the 1200W PSU, that to me are not needed, but some in the community like to have space. But i like the fact that FT05 is small, and would like to the see the new one similar, just an inch or two bigger, it would help a lot the GPU and PSUs choices for users.
3) Temper Glass, idk how this can be implemented on the design, but we have a lot of offering from other companies like Corsair, Phantek, to mention a few. Would be amazing to have an FT06 with an option of temper glass, and lets be honest, the aluminium used on the FT05 (which i love) is on the front and back, the side panels are steel, so changing them toward tempered glass would only add to an already great materials used, to me steel diminishes the FT05, but i understand why it is used.
4) Extra space on the back, we also need a little bit more on the back for cable management, it was very hard to do the cable management on the FT05, and still today i have to see that the side enters well and the cable don't move or ill get a belly on the side panel, and i don't have a lot cables running in the back and my psu is modular, only using what i need. A lot of newer cases are a breeze to do the cable management, there is no reason not to allow a little more space on the back, i understand the design and small foot print of the ft05, but im asking half an inch more than you gave us, its not much, its just too tight atm, btw i removed the sound dampening as this also hinder the space on the back, the case really need half an inch more or an inch if you are planning to include sound dampening, although i would prefer you give us temper glass.
5) Remove the CD option, save some costs, even laptop manufactures are moving away, take a loot into MSI GT73VR, the drop the Optical for another fan, the FT05 is a flagship, it should follow whats the tendency of the people that are looking for high end stuff and most likely this people dont use opticals anymore, save some money and invest it where it gives value to us.
6) A PWM AP182, this fans consume a lot of power, and even say they are not recommend for certain motherboard headers. Moving toward PWM we can get power form the PSU and use the PWM signal to regulate the fan RPMS, its a win win situation. Please if you do this, allow the fan to able to drop to 400rpms on PWM, i can do this atm with my AP182 but i have to move the knob to a certain 1/4 turn. I personally think that 400 to 1300rpms is a good range, at 2000rpms they are intolerable, never i have ever considered them to go above 1000rpms, they cool very good even at low rpms, i usually run mine at 400rpms and on load 800rpms. The big four motherboard manufactures (ASUS, MSI, AsRock and Gigabyte) have implemented great fan controls either on their bios or software, it can control PWM fans fine, there is no need for switches or knobs anymore, as long as the fan has a good range of control via PWM.
7) Forget about the 120mm fan on the bottom, there is no need for that tray, i understand the view of caving toward watercooling, but the fact is that the FT05 is the best air cooling case, and never will be a even a great watercooling case, it might be fine for some using 180mm rads as they have done with the TJ08, although for this to happen you do need a taller case, still i think FT05 is the best air cooling case in the market, and this is because it uses the AP181 (i use 182) and the direct flow it has toward the components, continue this philosophy, make the FT06 to be the best air cooling case in the market, i personally think the extra 120mm bracket on the bottom hinders some the 180mm fans airflow, and this come to deny whats the best of case, i would simply drop it. You can design a water cooling case from the ground up thinking on rads an pumps like phantek has done, but making the FT05 have some flexibility toward this to me its a mistake, if i go water ill go with a better water cooling case.
USB C on the front (top), the industry is starting to move toward USB C to be the standard, i know USB A is still the main requirement, so give us 2x USB3 A, and one or two USB C on the top, if the fans are PWM there is no need for Knobs/switches. The Fortress is a flagship and the best from silverstone, to me its only natural that things like this are included on the FT06.