Phoenix was really mean to Miles, but given what he lived throughout one year and the fact he knows nothing about what happened to Miles during this year (who won't help him at all to know more), a punch would have been totally logical.
He didn't because they were in a f*cking police station, little (already scared and traumatized) Pearl was there and because otherwise, Miles (maybe) wouldn't have helped Phoenix (so Engarde would have walked out free or Maya would have been killed), and certainly Franziska and more certainly Gumshoe would have physically destroyed Phoenix (that gave me some fic ideas btw) and definitely would NOT have been helped him.
So narratively speaking, a punch would have been a bad idea.
Still, if Ace Attorney was a multiple choice game, I'd have liked to see the bad ending due to that. Or what we have to do to still get Miles', Franziska's and Gumshoe's help.
But... it would have inevitably led to a drearier mood that's usually not proper to Ace Attorney.
Despite that fact the stories of that game mostly are grim and dreadful (that's why I love the 2012 movie, it reminds you that yes, the stories of your funny and light-spirited game actually are not).