Once Robert won the Iron Throne, do you think he should have done something to punish the Tyrells & Redwynes rather than pardoning them unconditionally (reducing their land, sending Mace and/or Mathis to the Wall, etc.)? Should he have punished Tywin, Jaime, Gregor and/or Lorch, and if so, how?

It’s tricky, because you don’t want to drive the former loyalists into one another’s arms and create an anti-regime coalition. 

The long-term play is to balance carrots and sticks, to give these houses just enough reasons to stay loyal while simultaneously weakening them in the long run. So instead of sending Mathis to the Wall, I’d order him to pay for a new royal navy, while offering temporary concessions on wine excise tax. And so on.