As I read your original post, I couldn't help but think of solutions for pretty much every concern you raised, so I'll provide some suggestions below:
<snip>
The campaign in a nutshell is this: A new, uncharted continent, the first established colony disappearing a year after it was founded. So, the only thing there Right Now are the Natives (and whatever past civilizations may have been wiped out, etc etc). The PCs are part of an expedition to find out what happened so a colony may be re-established, etc.
Great start. The natives provide some good role-playing opportunities and potential adversaries as well. Also a lot of opportunity for exploration and some mystery solving.
<snip>
Sure, the new colony will slowly grow, but it doesn't seem that there is a lot of room for Variety of plots/adventures, convenient ways to play with characters backgrounds* (since they're so far away from home), deal with rivalry with other humans that speak their language, etc. For instance, with there being no other colonies, there's no reason pirates would be here, so far from civilization, no threats from other cities, etc.
As others have pointed out, you don't need to go beyond the starter colony for politics, ambition, and intrigue.
Another problem I find is that since everything is UnCharted, there's no way to really point at sites of interest; the Pcs just have to wander around the map until they find them. So this makes local Legends, mapping, etc unable to really work ahead of time. You can't say 'Well here is a treasure map to a cave with a lost trove of fancy stuff over here' because, well, who made the treasure map and who told them this when no one's charted it?
Conversing with the natives can help to chart the area. Also, the ruins of wiped out civilizations are your friend. There's no reason that an ancient civilization couldn't have mapped out the island long ago. Imagine the PCs reactions if, while exploring some dusty tomb, they find a thousand-year-old table with a map of the island, complete with the names of settlements and temples and mines that have since vanished. Any one of those names may lead to treasure or adventure, and you can weave them into your campaign.
Granted, there is a little variety. They have to Get there, deal with being stranded, find the colony, clean out the inhabitants of the colony, find out why the old colony disappeared... THEN Making nice with the Nice natives, repelling excursions of Humanoids Wanting to Wipe Out the Colony, and wandering over the landscape, but I'm afraid after that's repeated several times, the PCs are going to get bored. How do I tackle this?
You need an overarching campaign theme with a definite resolution. Something that is an undercurrent to whatever the activities of the week are. This could be: defeating an ancient evil that has cursed the island (perhaps with the abyssal virus, which the evil wants to spread beyond the shores); building a kingdom from the wilderness to rival the established kingdoms of the old world; exploiting the island as much as possible to get all the loot there is to be had; bringing salvation and enlightenment to the savages; etc.
Once you have determined the theme and the criteria that determine its resolution, you can begin to create challenges that tie into the theme and lead toward the resolution of the campaign. The theme doesn't need to and shouldn't take front and center in every session or adventure, but it provides a guideline to you (the DM) on where the campaign should proceed.
Taking the theme of exploiting the island for example, you might decide that the campaign is resolved when the PCs can buy the rights to the island outright from whichever kingdom currently lays claim to it. You then know that the relevant challenges the PCs will face include things like common thieves, forged deeds of ownership, attacks on trade caravans, rival claims of ownership, and so on. You can easily tie these challenges into any existing adventure, so that the PCs are free to choose where they go and what they do while you still guide the campaign toward a resolution.
Another problem is Character Choice. Sure, the PCs can point at the map and say "Let's go in that direction", but beyond that, where is the freedom for them to establish goals and move onwards? What options can I Give them?
This is one of the reasons you need a campaign theme, it helps you to decide what sort of goals you can present to the party. As others have said, the fear of railroading is misleading. Most players are much happier with a small number of choices than with a completely wide-open world with nothing to guide them. Just make sure that choosing the theme for the campaign is a collaborative effort. You want the players to be excited about challenges that further the theme.
One idea I had was to have PCs go into a tomb/etc, trip a trap, and basically be put in stasis for about twenty years. So when they come awake, they find that the colony has grown in size, neighboring countries have set up their own little places, and now it's a lot more like a town on the frontier, lawless, and it can be played like the French and Indian Wars. But that seems a little ham-fisted.
I'm not sure something so drastic is needed. It's perfectly ok to say "For the next 2 months Bob surveys the surrounding landscapes, Kate works on translating the Oompa language, and Dave studies the flora and fauna of the island. Nothing exciting happens." Allow time to pass in the game, and you can allow the world to evolve more naturally.
<snip>*Well, two players actually have set their background to be in one of the Houses that financed the original Colony. Said House I intend to be one of the ones putting the expedition together, so I could bring in people who know these two PCs. Even so, that's not too much background to play with.
It's hard to provide suggestions without some more specifics, but the campaign theme can be a guide here, too. Perhaps one of the PCs has an uncle who works as a moneychanger in the old kingdom, and he can act as a fence for their native works of art and exotic goods. When one of the artifacts turns out to be an heirloom of an old noble family that mysteriously wound up in the hands of the natives, the uncle is accused of theft and the PCs are embroiled. Will the uncle keep mum on where he got the artifact? Maybe, for a price. And just how did that artifact get there, anyway?
Overall, I think you have a wonderful setup for an interesting campaign. Just don't be afraid to create challenges on your own. Let the players decide which ones they take on and which ones they avoid, and create your next set of challenges based on the players' decisions.
