Well, this bothered me in the original games too: They replaced the tower in Lavender Town with a freaken' radio tower! I've always found this very distasteful. It's like "Oh, here's this tower honoring dead pokemon. ...It's too creepy... HEY I KNOW LET'S TURN IT INTO A RADIO TOWER!11!!!"
Seriously? And people think building a masque near ground zero is offensive? This is worse, IMO. -__-
It definitely was very disrespectful of them to move the Pokemon from their resting place and then turn it into a radio tower. I mean, don't we often talk about "honouring" the dead? It doesn't seem very unhonourable to destroy the Pokemon's graves (unless the people of Lavender Town don't think Pokemon deserve honour...)
And the fact that the graves are now in this small house seems disrespectful as well. The game says that there are many chambers there that only Mr. Fuji can enter...if that's so, then how can the trainers of the Pokemon buried there visit them? And why can other people only pay their respects to the Pokemon buried on the first floor only?
It doesn't make sense that they did this. I hope that the Radio Tower is haunted.