Was George Orwell an Optimist?
The Herbie Nichols Project - Dr. Cyclops' Dream
*I need to remove all 8 merchant tokens myself before they re-spawn forcing me to move a lot around the map and the juicy locations re-spawn very rarely.
That is more than balanced by the fact nobody else will take them before you get there.
*I can't really hunt all 3 players, I could probably annoy one or two players mostly being a spoiler/kingmaker but not helping myself much compared to the cost/risk of PVP combat.
You need to pursue your own goals more than hold the Merchants down anyway. You can focus on whoever appears to be ahead, and make the others nervous.
*Cards targeting pirates only target me.
What cards? It's not likely you'll be fighting all the other players anyway.
*Fleets only hunt me, and they are generally stronger and more numerous than NPC pirates.
Fleets hunt pirates. That's true regardless. And they'll attack merchants too, if the two nations are at war.
Of course being 1 merchant and 3 pirates might make the merchant's life hard especially if the other players perceive him as the favourite to win from the start.
This is more of a real issue than the things you listed about 1 pirate with 3 merchants. With 3 aggressive pirates, a single merchant will have to stay on his toes. He'll be less likely to see in-demand goods delivered to ports just before he arrives, though.
I play to the strengths of my own captain and don't worry much about whether there are equal numbers of merchants and marauders. There's room enough in the Caribbean for everyone.