Two problems for me:
1. No included fans(this case is not very cheap, so fans just add to the expense for those who aren't watercooling).
2. ATX motherboards are supported, but ATX power supplies aren't. I know the two might not have a correlation with each other, but no ATX PSU support shrinks the compatibility options quite a bit - especially for people interested in porting their old ATX power supplies.
This market segment and price bracket doesn't need included fans; People will be choosing their own fans and I always end up replacing the included fans because it's almost impossible to source matching fans of the type that are included. BeQuiet and Fractal are the exception to this as their included non-RGB case fans are usually the type that you'd actually want to buy more of - yet that only applies if you're buying a silence-focused non-RGB case in the first place.
Most "free" fans included with the case are garbage-tier sleeve-bearing fans and, unless you're making a budget build where you'd only be buying garbage-tier fans anyway, are not worth keeping. Chances are that the free fans included with a case will need replacing in a few years anyway.
I agree with your second point, but it's a necessity of the layout. There are other case variants in the O11D lineup that support full-size ATX PSUs so if you're intending to transplant a decent ATX PSU across from another build, you should just pick a larger case that permits that.