My nav bag is an old yellow surplus canvas satchel. Much better than those bloody large black cases you see people with. Mine can be positioned between the front of my seat and behind my legs without interfering with anything. Everything in it is accessible in flight.
If not flying it can be slung over my shoulder.
I'm beginning to realise that something like that is the answer. On our recent trip to Salzburg in a C150, we were really tight on weight and balance. I had all my gear in a large holdall that would convert to a backpack if we needed to walk out of any small airfields. Within that I had my flight stuff in a cotton carrier bag, to save on weight of course. Well, it was wonderful. No carting heavy flight bags around, just grab my carrier bag and sling it on my shoulder. No surplus stuff hidden in pockets, only what I actually needed, and easy to find. And, as you say, can be put in front of knees, or hung on something, so easily accessible in flight.
Maybe simplicity is the answer. Unlaminated maps that fold easily, and basic carrier bags. I know someone who carries that to kneeboards too - a piece of paper and a pen in his sleeve. But I do rather like my tri-fold, lots of pockets, keep everything in it, kneeboard...at least for now.