"Why we need waypoints in the starter cities? You already have Teleport Earring that you can make very easily. "

Otherwise known as inventory-1 in a game that already heavily restricts inventory.

"You can also use the VW port from VW NPC to just the doorstep of each of the starter cities."

Some people put a lot of work into their mog house, or simply prefer not to live in Jeuno. If I live in my starter city, I have to make a series of jumps to Jeuno to use the waypoints, effectively eliminating their usefullness as a convenience, which seems to be the entire point.

Don't see any reason why not to have a waypoint in starter cities, even if only takes you to Ru'Lude Gardens.