Lots of good answers here, but I just felt the need to add my two cents in, even though it may be a little late to the discussion. It's my usual reply: see what feels good for you.
Generally, the problem with cushy, supportive footwear is that it hinders proprioception (http://en.wikipedia.org/wiki/Proprioception), that is, the body's ability so know what's going on elsewhere. Often in the case of footwear, since the padding and support get in the way of your body knowing whats really going on with your feet, you'll have symptoms like less balance and stability all the way up to knee and hip pain.
Now in your case, since you're overweight you MAY need some support, going barefoot may hurt your feet more than help. But you can't know that until you try. You already know how you joints feel with shoes, so take a week or two and see how your feet feel without shoes. If the overall result is less pain or better feeling all around, go with it, otherwise, maybe go back to shoes and ratchet down the padding and support as you lose weight.
I know that when I switched to motorsport shoes (that help you curl your toes around the pedals when driving), the thin sole really helped my balance. I now go hiking in flip-flops rather than boots and I can go longer and faster with absolutely no hip pain, when before I'd be sore for days after a long hike. So for me, the less shoe, the better. But see what it's like for you.