Here's what I ended up doing:  I let him keep the character as-is.  I
didn't feel like having to go back and rewrite posts, and counting
myself we only had three players.  I've also told him that as a
consequence of training himself to such a degree, his Pokémon training
skills would have to suffer.  (On that point, I also gave the Trent
Retwin example, but I left out the name)  However, I couldn't think of a
good reason for him to not have all that beyond the fact that it
offended my sensibilities.

My plan, however, is to adjust my campaign (which I'm just making up on
the fly anyway) so his enhanced character becomes a liability.
Basically, I'll have to make sure his power is completely uncalled for
in every possible situation.  The two approaches I'm considering is that
any villain he faces is so unprepared for direct attacks that using that
tactic loses its glamour, or stepping up their game to the extent that
either his power is completely canceled out or everyone else suffers
from the extremeness.  Since I want his character toned down, I'm pretty
sure I'll have to go with the first option.  The second option just
promotes power gaming.  Considering my other player's character grabbed
The Fury by the neck (despite Fury being described as a "little girl")
and threatened to kill her if she tried to harm his friends, it's not an
inconceivable notion.

"Omnipotence is baaad".

You've been wearing weights?  That doesn't make you that strong.

One of the tenets of the Pokemon world seems to be that pokemon are
naturally stronger than humans.  There are definitely a few exceptional
humans that are stronger than the average pokemon - but the logical
conclusion is that the strongest of pokemon are, in turn, stronger than
even these humans.  Furthermore, anyone in that excellent a physical
condition would be obvious, to the point that Team Rocket would have
brought such a counter-pokemon along to deal with him.  (And if it
really was their first encounter with Team Rocket, how would he have
built up a murderous grudge?)

But the more serious breach is that the author is adding powers to his
character with no previous logical justification, specifically to make
his character unbeatable - as in, omnipotent.  ("Previous" as far as any
reader has seen, that is; not "previous" from the character's newly
rewritten history's point of view.)  Even predeclared power is not as
bad (because then other authors can know in advance that battles might
not be winnable, and avoid confrontations - or any other interactions -
with the overpowered character, unless they see a way around what has
been declared).

One possibility is to pull in NPC gods, or otherwise overpower the omni
PC in ways that do not significantly affect the other PCs.  In this
case, perhaps TR had backups - hidden "offstage", but on hand to deal
with this guy.  If he hates TR, TR might well know about it and have
been using The Sound and The Fury as unknowing bait.  They spring out,
overwhelm that guy, then move on leaving everyone else to deal with
their situation.  That guy is then removed from interaction - further
stories involve him and NPC TR members only, and can be forbidden (or at
least frowned upon) on the basis that he's no longer interacting with
the other PCs.  It takes caution to do this without going omni; I've
done it myself more than once in a certain PW!-like game, and made sure
I only went omni in response to someone else going omni.  (Which is
perhaps one reason why I like shapeshifter characters. ^_^; )

Another is to go meta and declare rules breach: the character is
acting OOC relative to what's in his published Writer's Guide.  Major
revelations that add new powers simply aren't allowed.  (Consider PW!'s
explicit warning against being a more powerful psychic than Sabrina.)
This is less satisfying, but it is much easier to do and does get the
message across with little chance of confusion (and does not risk
accusations of the same ill act being sent to the corrector).

The approach you went with (making the power useless) is attractive if
you're seriously hampered for players - where you have the time to give
that amount of attention to one case, over a long period.  That's not
the case with PW!, but it's definitely suitable for the more common
players-and-GM RPGs.

Personally, I wouldn't have included the PW! tags at all, using only your
own PokeOps tags.  I'm sure everyone who's read this post would have read it
regardless of tags, and that way it would've been less misleading.

I suppose it'd be pointless to mention that such heavy weights would sink
HIM into the ground, regardless of how strong he was.

Personally, I like the Rob-and-Tymes standard RetCon Machine.  Add more
information to the story in a follow-up that undermines the offending rules,
with a note that the author should take your example to avoid more severe
punishments.  You can't always do that, of course, so the best bet is to
post a standard NS post telling the author to RetCon his OWN story to fix
these problems.

The fact that he left the details out of his WG is annoying, yes, but
bad/flawed/rulebreaking stories are a bigger crime than incomplete WGs.
Ergo, he should be told what he did wrong and how to change it.  If he
doesn't learn his lesson, he should be told again.  Finally, if he continues
to resolutely break rules, he should be banned.  Very simple - this is
SHAKKmaster's story.

Of course, being forums, I'd apply different rules.  Threads can be locked,
posts can be edited or deleted, and members can be banned.  The AGNP methods
should still apply, but combine them with threats of forum-based actions.
That's what I'd do in your position.

Steffan