Hi Craig
I won't talk about mesh, as I use a manual install of Vector Land Class, but I guess that the most popular is Orbx NZ. Note though that Orbx does really need to go into your Prepar3d installation, which does bypass the recommended install methods.
There are Subscription installers for Prepar3d v3 now (anything listed as a 'multi-installer'), and I'd certainly recommend that you get them if you don't have them already. It means downloading everything again, but it does use the recommended install method for Prepar3d v3 -- the Subscription installers let you choose the initial location for a 'Godzone' folder which will include all the Subscription scenery, and any other Real NZ or Godzone scenery released from now on (and including Nelson now). The chooser displays the first time only, so you need to give some thought to where you'll put your addon scenery. The recommended method is to keep it separate from the Prepar3d installation, so if you have a specific drive for scenery then you can choose that. For people with only one drive, the default location, which is outside the Prepar3d install, is sufficient, but you can choose any drive/location based on what's going to work best for you.
There some info on the multi-installers here.The multi-installers also use the new Prepar3d v3 method of activating scenery, bypassing the old scenery.cfg edit method which some people are wary of. Note that the multi-installers will automatically deal with scenery priority, provided you install the issues in order.
However if you don't want to redownload everything, you can use a migration tool, such as Estonia Migration. This is a good tool to have anyway, as it helps install older stuff which doesn't have an updated installer. Note though that the older installers will install into Prepar3d, rather than the location of your choice.
Clouds/weather isn't as simple, there are a lot of different opinions around. I use AS2016 and ASCA, which replaced REX Soft Clouds and ASN, and I'm very happy with it.