In my humble opinion, there should not be dedicated 3.5" HDD rack in the central part of the case. Instead, it is better to have additional 5.25" bays, where 3.5" drives can be mounted in removable cage (like Coolermaster did in their original Stacker design). This approach has the following advantages:
1) It is more flexible - you can use available space for whatever you need - 5.25", 3.5", 2.5" devices, reservoirs, or even install additional radiator in front of the case;
2) Front intake fan will work more effectively without having to blow through drive cage walls spanning across the case right before it (instead, we get some sort of the duct formed by 5.25 bay walls); Having a lot of spare 5.25 bays allows to install not 1, but 2 intake fans, which will more than compensate decrease of fan size;
3) It is more future proof - we are going to use 2.5" SSDs soon

, which are silent and cold, so they can be stuck just to any side of the case and dedicated 3.5 bays will be totally wasted;
4) Integral side walls of 5.25 bay area will make entire case more rigid;
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