Stock SE4 is pretty terrible in terms of balance, creativity and general sense-making (balance naturally being the greatest concern). It was pretty much a bad conversion of SE3's data, with some new items added here and there.
The MM mod site will probably always be empty. I'd rather keep the
Wiki up to date, personally.
For the most part, the mods are posted and discussed on the se5.com site, rather than here. A few of the old guard try to keep Shrapnel in the loop, but all of the new people are over there. There is a stock game AI mod. There are a few mods of the "Devnull" tweak stock and add a few things variety, etc. There is a BSG mod in development, and some talk of a SW mod (though I don't think any real progress has been made on that front). P&N would be pretty boring to reimplement, which is why I suspect noone has really done it yet for SE5. The amount of mods available seems to dwarf what was around 10 months after the release of SE4 (largely due to a much larger initial install base, but still).
Honestly, I doubt Aaron would have given more care to the stock data set if the game wasn't made so moddable. Its not like it takes any extra effort to mathematically balance weapons et all from the get-go. I think he would have just spent more time on the graphics engine.