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custom taxonomy equal with category (key = 0), post tag (1), nav_menu
(2) & link_category(3) - they are still taxonomies, but from nearly
every use case with the wp_taxonomies array it's just ... non-handy.
In most cases you won't set the build in taxonomies equal to your
custom ones. You registered them, because the build in stuff didn't
fit your needs. With the current setup there's the need for some ugly
work arounds/hacks to exclude the build in taxonomies. It would really
make sense if custom taxonomies would reside in only one array (key 4)
and therefore be easier accessible/loop-able. Going one step further
and registering this new array as a separate global available $var
would make even more sense.

So here goes my question to all people who have enough in-depth
knowledge: Would this be possible or is $wp_taxonomies that deeply
nested, that changing this is impossible?

Thanks.
- Kaiser.

Ps.: As you can read in my statement before the code, i wrote it
without testing. I hope the guy who asked the question will edit my
code and replace it with his, so don't kill me for this (verbally).

[1] http://wordpress.stackexchange.com/questions/9060/it-is-possible-to-get-a-list-of-post-types-asociated-to-a-taxonomy/9064#9064