The graphics, they have been actually doing more with the graphics this time with the remakes than they had done with DPPt. For starters, the basic 2D and 3D combination works perfect for the game, and isn't anything I would personally complain about. On the topic of the trees, whether it be skinny, fat, tall, or shot they still have a good appearance to me. Trust me, if you don't like these you really wouldn't like to see what else can be done, and yes it could even get worse. In my opinion though, I don't mine any of the trees how they look with the touch of 3D, as it isn't something majorly affecting my game play. It looks decent enough and it is just there for its story and show, so nothing much is to say about it on my part.
As for the bag, it was shown that Gold was standing when the players view their bag. Now, this doesn't happen to be my favorite scene of the 3D use because it really did not look all too well in display. However, I can see that Game Freak is really trying to bring the 3D look to the games more and since this is basically a first time try out, I don't think it was done terribly. It is something tried and I think it'll work out fine. My favorite use with the 3D design would have to be the cut scenes with Lugia and Ho-Oh. This actually shows motion and the way the distributed Ho-Oh and how it flies actually turned out very well. Not much motion was shown with that of Lugia, but it still came out with a nice touch. I'd like to see more 3D effect take part in the game, because so far nothing seems terribly. Except, my only nitpick is the grass and its depth that someone mentioned earlier. It did become a little too extended in thickness with the use of 3D, but I think I'll be able to live as it is basically only the grass we walk through.