The whitelist was a great server with capability for a range of playing styles, but the number of mods really did slow down load in. My observations and how they relate to the PvE server and it's current mod load:
The Good: IMHO a lot of the larger mods cross over nowadays and complement each other, S+ and AA have largely the same crafting and utility items, however each mod has their own advantages such as AA provides a tek style wifi generator, which can power the S+ farmer, gardener, nanny etc without the need for their specific fuels. Removing S+ or AA would be detrimental to the server. The stacker mod is handy, particularly when you get established and develop larger farming regimes. The fog remover is essential particularly on Rag (they still cant remove water fog though LOL). Death helper and pet helper are useless until you have an incident, where they suddenly become the most important mod in the game (game crash whilst flying?). Wooden hanging bridge is nothing more than a bit of fun.
The Bad: Joans Egg and Poop Collector
is still the most reliable collector of it's type, but it could probably be removed now as S+ and AA both have the same functionality. TBH I haven't seen the S+ collector in the engrams, so it may need activation however it should run on the AA wifi generator if someone specifically wants to use it (I certainly would).
The Ugly: Eco's mods were fun however I found a lot of misalignment in their structures, far more than S+ has. As an example I built a huge stable on Ragnarok which took me days, when it came to the roof (which had a significant number of panels) a small number would not snap. Incredibly frustrating and I was unable to get around it. All of the mods ask that they be loaded in first, particularly S+, or the structure snapping can be affected. Multiple building mods could become an issue for the player.
I have my theories about how to cater for this, but it involves clustering the Center back in and it all requires extra work for Munki so I will withhold these for now.