In the patch, having over 20 provinces as a Merchant Republic reduces Republican Tradition. By a LOT. Having barely 30 (which is, in some places, still grants too little development to upgrade government rank to Kingdom) is enough to prevent a merchant republic from gaining any RT over time at all! (The penalty is 1 per year, the exact same amount a normal republic gains.) You could get around this by granting more land to vassals... but if they get too big they'll gang up and declare independence.
One thing that wasn't changed, is that Merchant Republics are still explicitly forbidden from switching government type. No Oligarchic Republic for you, Venice. So if you like playing republics, have fun playing as a HRE minor or the Netherlands, because all the others are dead, dead, dead.
And if you wanted to play around with the trade league mechanics you paid money for, well, enjoy sitting on your hands after gaining those thirty provinces, watching the world shift without you.