I think Catholicism is quite good. True, you don't get any morale or discipline bonuses, but you arguably get the same monarch points as Protestant through the -inflation and +stab actions. You really need to go for a lot of cardinals, though, or devoutness, or be a nation that has +Papal influence, to get the most out of it.
IMO, Reformed is the most questionable of the Christian denominations right now, at least for me. When I go Reformed I tend to end up with the fewest monarch points, as I have to spend admin to get to +3 stab to keep one of the powers active all the time. Personally, I just find Reformed annoying, with the save-and-activate style, I would rather just keep something active all the time.
Here is how I would change Catholicism, though, to answer the OP:
All it really needs is a change to the decision "Embrace the Counter-Reformation."
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+3% missionary strength vs heretics
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+0.5 Papal influence per year
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+2 missionaries
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+5% technology cost
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+5% idea cost
I would get rid of the 2 missionaries, the idea and tech penalty, and add +2.5% land morale. Then you make another of those "only good decisions" everyone gets. The morale will make Catholic good for countries without additional +Papal Influence. This decision would also give
everyone an extra +.5 influence to everyone post-1500, and make the religion extremely good for countries with devoutness or national +influence.