I would break it up thusly:
Questions asking about user-generated tweaks to existing systems.
I don't really see an issue with having this tag cover analysis of existing mechanics and the creation of new ones. Both are an application of the same skill-set. However, it may grow to become meta if we develop a more refined set of sub-tags.
The distinction I would use: game-design is about generic principles, and the creation of mechanics for outside use. house-rules is about tweaking existing systems and mechanics for personal use.
But I haven't sifted through those tags yet to double-check.
The one that feels a bit odd is homebrew. This question should probably be tagged house-rules:
Players rolling all of the dice in D&D 4th Ed
This question might be tagged house-rules or game-design, depending on whether you view the One Roll System as an engine to create new RPGs (tag it game-design), or a consumer-usable system in its own right (tag it house-rules):
Adding an explosive dice mechanic to the One Roll Engine
That leaves the question: is homebrew about rolling your own things in an existing setting, or is it a system tag about playing with a custom-built system (a la dnd-4e, 7th-sea, etc.)?
These questions support the former:
Guidelines for creating homebrew classes (base/PrCs)
Custom magic item creation standardization
Are there any low-magic 4e home-brew settings?
This question supports the latter:
What tool(s) have you used to manage spell lists, especially in a home-brew?
I'd lean towards using it as a system tag, but the actual usage leans towards using it to describe user-generated content. I'm also not sure how the homebrew and systemless communities interact... Whether systemless gaming is truly without rules, or if it can fall under the umbrella of a group-specific customized system.