Even if it was only to get G/S/C Pokemon into the 3rd gen, it was a huge success, and I'd love to see another one. I hope they'll bring back the Gym Leader challenges, and let Triple Battles in there too. I really think the shadow Pokemon games were the main foundation of Double Battles(where people got good at them and where they most mattered).
For PBR, I want to see something better than it, because PBR is a pain to navigate around, and so is making Trainer Cards. At least make it faster and easier. I'd love to see more effort put into it as well.
PMD, for me, it got kinda boring after I beat Darkness. Maybe if they changed the plot, and added some events, then I'd play it again, but all I really want to see change is the plot.