Why didn't you include (name of mod)?

It's possibly an oversight. Leave a comment explaining how it meets the mod list criteria.

I recommended a mod but you still haven't included it or explained why.

It might have a deal breaker of an issue and I'm not willing to publicly trash-talk other mods. If it's any help, I happen to agree with most of what's written here.

I looked it up and some of the mods on the list are outside the top 500 on "Top Files".

Indeed. It takes a little over 3 endorsements per day to hit the top 500. The rankings outside the top 300 can fluctuate wildly. A mod that was ranked #400 at the time the list was updated may only be ranked #750 now (the difference in rank #400 vs. #750 is only 1 endorsement per day). And next week it may be ranked #375. Here's the breakdown:

Amount of endorsements received over the past 2 weeks required to land in the....

Top 100: 110 endorsements (8 per day)
Top 200: 80 endorsements (6 per day)
Top 300: 60 endorsements (4 per day)
Top 400: 50 endorsements (3.5 per day)
Top 500: 45 endorsements (3.2 per day)
Top 750: 35 endorsements (2.5 per day)
Top 1000: 23 endorsements (1.5 per day)

These numbers are approximate, and change over time with Nexus site traffic, which has seasonal fluctuations. In the event you're reading this many years later and this is no longer being updated, the above numbers will decline over time as Fallout 4 gradually loses popularity.

When a mod updates, its endorsement numbers typically spike for a bit. Mod categories also move in cycles. For example when a big quest mod releases, it tends to raise the rankings of many other quest mods along with it, as players who play primarily for quests are drawn back into Fallout 4.

Once a mod goes on this Mod List, it doesn't come off until something more popular replaces it. Even then, while the most popular option is generally listed first, an alternative is listed after that where feasible. Alternatives will frequently fall outside the top 500.

There are also a couple instances of mods on this list that are compilations of an author's work, where the individual components are more popular than the compilation. I listed the compilation instead of the component to save plugin slots and installation hassle.

I see a couple mods on here that haven't been released for a full month or aren't on Nexus at all.

I count release date as release date, not Nexus release date, although usually the two are identical.

There are mods like "Creative Clutter" on the list that were once quite popular here, but the mod authors removed the mod from Nexus and now host it on a different site.

There is one instance of a simple mod (i.e. it doesn't really need mod support) where the author disabled comments because of trolling and also disabled endorsements, but the rest of their work is popular, and if you apply a standard endorsement ratio to the number of unique downloads, it qualifies.

This sounds less and less objective the more I read about it. I want an asterisk-free list.

Fair enough. Feel free to leave constructive suggestions in the comments section. Although the Discord server is typically a better avenue for discussion.

The description says you run over 500 mods personally, but there's only about 250, give or take, on the list.

It's a popularity-based list, not a personal one. Over half the stuff I run personally doesn't qualify for reasons of either popularity, bugs, compatibility, copyright (e.g. music in a soundtrack replacer), or lack of mod support.

I installed this list, plus some other stuff, and while I can load my save, I can't start a new game.

This can be caused by mods that add items to your inventory right away, or by dialogue interface mods. You can try to pin down which mod, but some alternatives are:

(1) Start the game in vanilla, directly from the Steam Launcher, without any mods. Save right after character creation. Exit. Then reload that save with all your mods. You get to redo character creation before you leave the vault, so you aren't locked in to the initial character creation.

(2) Download a save game from Nexus. Usually ones right after character creation, or right before you leave the vault, are the most useful.