The tower is in an improvement, jagged as it is, I never liked the bike pits. The tiny cave that plays the Mt. Chimney music solely to acknowledge that that used to be Spear Pillar's tune too was a nice momentary touch. Deoxys in space was an impossible dream.
The dragon worshipers were awkward; aside from those spectacular carvings the only thing they exist, or fail to exist, to do is to give Zinnia a ton of authority in a really, REALLY short amount of time. Which is unfortunate because Hoenn is a region where that kind of story makes sense. You could have scattered a few more whispers and remnants around to build interest throughout the story proper and really throw off the people who already knew the GBA games by heart.>>35963683
As a former kid who missed that dialogue at the time? More likely than you'd think. We can quibble about jumping to Mauville but the rest was a big improvement.