I've always really liked R/S/E's intro but, honestly, that's nostalgia talking, lmfao. Of course, though, that intro has always just been really cool. I also really like Platinum's intro, and HG/SS's. B/W's is good, too, though. But, tbh, everything after that is pretty boring and not really that memorable to me. =/ Except maybe OR/AS's. Most of the 3d era Pokemon intros just aren't that great, imo.
Also the absence of the Pokemon theme in the press start menu of D/P/PT has always struck me as odd, but the opening cinematic makes up for it, I guess?