Mick,

You have great case design here. Realize that there is no way you'll satisfy everyone's desire though. That's the nice thing about modding cases. If you don't like it then mod it.

I think you are on to a very flexible design. If someone doesn't like 3.5" bays it should be easy enough to swap it with a 5.25". If you don't want the bay turned sideways then mount the other way around.

My one suggestion to make the design a little more flexible would be to put a fan hole on the bottom of the PSU tray so you could flip the PSU over if you didn't want the fan facing up.