First off, some background: I've been an administrator on a site that was similar size to this (I think I've stated this a few months back) and have experienced quite a bit of what it's like to deal with large websites and communities. I also have sufficient web design knowledge and can code fluently in XHTML, CSS and semi-fluent PHP. I am very familiar with the ins-and-outs of web standards, too.
Lord Kokkei, I have to say, you're horribly misguided. You speak of Web 2.0 and W3C standards as if they are the be-all end-all of website design. Yes, coding by standards is always preferable and yes webmasters should try to follow them, but with a site like Serebii with thousands and thousands of pages, revamping them to match these relatively new web guidelines would be a futile task. It's been already said, but the time spent doing it would be much better off being spent adding to the content - especially since Serebii is driven entirely by content.
You say Serebii is ineffecient. How so? If I wanted to, say, visit a page about the D/P Elite Four, it takes me TWO logical clicks: Diamond/Pearl --- > Elite Four. Exactly the way it should be, and that's just one example. You say Serebii is old. This is ridiculous and irrelevant. My grandma's old, does that mean we get rid of her and replace her? You say Serebii is clunky. Albeit, while this is true, it is also inevitable considering the sheer amount of pages that need to be constantly referenced. For the most part, the server speed also makes up for this fact.
By spending dozens of hours validating the entire site, it would do what, exactly? Cut load times by 0.2 seconds? Hardly worth it, at all. Contrary to what your little webinars and keynotes have told you, Web 2.0 and web standards aren't always necessary, and often by following these standards the users won't see any benefit.
Also, calling Serebii arrogant is also a bit rich. You seem blissfully ignorant as to what running a site of that caliber takes, and considering you've got no experience yourself, I'd stop telling him how to do things. Your know-it-all attitude really is driving me up the wall.
If it's not broken, don't fix it.