Oliver Hazard Perry leader counter from Amateurs, To Arms! by Clash of Arms Games.
Warrior Band counter for Conquest of Paradise by GMT Games.
Some explored islands could come with local warriors
I've already incorporated this idea into the Solitaire Rules. You can find it here:
(the counters for the Solitaire Rules are here):
...and/or with malaria(which would be visible only after colonialisation)?
Well, malaria is only endemic in Melanesia, not Polynesia (nor Micronesia)- to this day. Anopheles mosquitos never made the jump to those islands. That said, I must admit that the Malaria rule in Conquest of Paradise doesn't come up much; players simply do not attack into Melanesia very often. So perhaps a very un-historic variant with Malaria in Polynesia might be a fun addition to the game.
Also the board could be more balanced non historical one, perhaps with 3 players with islands close to each other in the middle,
I suppose that this could work, but I very much prefer the historically correct start points, and think they work rather well.
...now the 2 players close to each other have disadvantage.
Do they? Others have posted (often quite emphatically) that Samoa and Tonga have an unbeatable advantage because they start with an economic advantage on their home islands, and are not as dependent on exploration, since they can invade Melanesia and Micronesia. Personally, I think that the disadvantage that you state and the advantages that I state perfectly balance each other out.
Or players starting from side and open ocean in the middle.
Sure, you can have the Polynesians coming from the west vs. the Peruvians (the discredited Thor Heyerdahl theory) coming from the east vs. the Inuit (what if they had expanded south instead of east?) coming from the north vs. I-don't-know-who coming from the south. Antarctic aliens?
Fun ideas; thanks for posting, Joonas!