1.Lenora quit because she wanted more time to spend with bones.
2.Dragon Spiral Towers Pokemon are higher levels because you can only get there after defeating the elite four and the champion.
3.The cold storage was replaced with PWT
4.Twist mountain is still there but it collapsed at one point.
5.Route 10 is closed because the old Victory Road collapsed, Route 10 is no longer in the game even if you use cheating devices to get by the road blocks you will see nothing there.