Just my 2 cents:
I don't think we need this kind of deprecation-warning filter in core.
As far as I know deprecation warnings are never shown more than once for every method, so it isn't going to pollute or obfuscate the error output when you're working with the code.
And users/production wouldn't be seeing them anyway, right ?
And if you maintain compatibility with an older version of MediaWiki, you might also find it useful to raise $wgDeprecationReleaseLimit ocasionally to only if there's any usage of more problematic / longest deprecated methods, and lower it again when you want to see them all.
-Krinkle