User blog comment:DaNASCAT/Technical Update: November 26, 2013/@comment-188432-20131127222615

From a strict typographical standpoint, H1 is for the page title, only. For a page to make visual sense, the title must be bigger than the section heads. Ultimately, that's why Using an h1 for a mere section head is explicitly against: It's implicitly contrary to:
 * Wikipedia manual of style, which is relevant to not only by virtue of general wiki precedent, but because some Wikia wikis simply defer to the WP MOS. Examples: w:c:marvel:Marvel Database:Manual of Style, w:c:vintage patterns:Vintage Sewing Patterns:Simplified ruleset
 * tardis:T:HEAD
 * memoryalpha:Memory Alpha:Manual of Style (headings)
 * w:c:wowwiki:WoWWiki:Manual of Style
 * w:c:harrypotter:Harry Potter Wiki:Layout guide
 * Memory-Beta layout template
 * various automatic page-generation templates at w:c:eq2, such as w:c:eq2:template:LnLInformation
 * The fact that most every single page on the whole Wikia network does not employ H1s as section heads.

So the reason that the TOC did not include H1s by default is because it is actually wrong to do so. The fact that an H1 section head didn't show up was a kind of warning to editors that they'd gotten something wrong. Moreover, it prevented a simple typo from ruining a complicated table of contents. Now, what was before usually a typo has the potential to displace an entire TOC's hierarchy a level.

A TOC's failure to recognise H1s was beneficial. It was not a bug, and it definitely didn't need "fixing". It helped to enforce local rules and prevented a common typo from having a completely unintended knock-on effect. I've yet to come across a single wiki that has bothered to create a manual of style, or guidelines about layout, that hasn't outlawed, at least implicitly, the use of H1 section headers.

Please rethink this.