So for example, I could have a skylands portal for every world, in addition to the nether portal, except the skylands is made out of water and lightstone or something.

Not sure this is the right plugin to do this, as I'm pretty sure there are already other small plugins that do this. Will report back later.

I agree with multiple links.
I too have a sky island world and would love for players to be able to create a portal out of quartz blocks and light it the same as nether portals and be transported to a relative position in the skylands.
Maybe have an option in the config for which block id used for the portal links to a specific world?

I would love to see this feature in Multiverse-(Nether)Portals as it is the to go to Multiworld plugin atm.