How do you prepare against stupid rules, blatant cheating being allowed, and the author wanting to fuck you over?
You can never prepare for everything, and Brock spent months preparing for this fight, only for the author, who is effectively an omnipotent god of the story, deciding to go "nope".
He did spend time preparing, but it was time where he was massively overcommitted and having to deal with all breeds of nonsense. Then, a week before showtime, a bunch of his A-listers get benched because someone decided to piss off the mightiest fire chicken.
At the end of it, Brock had a team one third full of his elite "rookies" in Gawain and Jormungander, one third full of pokemon he works with significantly less in Tide and Shrek, and finally Titan and Knight, his actual elite mainstays. Meanwhile, Will got to bring his fully rested fully tuned team of 6(7?).
Brock managing to salvage a draw from this fairly disasterous battle with a desperation move of all things(he had no clue Shrek could use Darkest Lariat) is pretty spectacular in and of itself.
Discounting the cheating from the other side, Brock was more than a little sloppy with this one. Thinking back on the fight, nearly every exchange was a pyrrhic victory. I can barely remember what Knight contributed during the battle, and he is one of Brock's mainstays. I think that says quite a bit about how wrong everything went.