Here's a minor "completist" F.A.Q for those who want it. I wish I had this before playing the game, but if you aren't keen on replaying the game from the beginning again, check it out.
I personally started over after I did Harbor Town first, after I found out that doing so had trashed an entire section of the game.
A player who wants to explore Risen as much as possible should do the world in this order;
Spoiler
1. All quests in Swamp up to meeting the Don, do not ask Cormac (at Don) about mages and do the first 4 quests for Fincher (at Don);
a) Conquest of the artifact camp (tip; go around with your "army" for a while to collect xp and loot if you like)
b) Salvage work
c) Tell Fincher about the strange temple entrance in the east
d) Treasure hunter wanted (in your journal, not completed)
Do not speak to Cormac (at Don) about mages so you get the quest "Talk to Master Illumar". If you chose to play mage later, it will never complete.
You can learn Pick Lock 2 and Pickpocket 2 in the Swamp. They are great to have before entering Harbor Town and it's the last chance to get them if you make certain decisions in Harbor Town in order to become a mage.
2. When entering Harbor Town, do not speak to Delgado (shady character near the back entrance) until you completed the Farmer's Sick Wife (probably first quest you get) 100%. This is a key quest for becoming a mage (completing it requires speaking to Costa either before taking the quest from Delgado, or resolving the quest which requires you to pick between Don/Sebastian).
Now explore Harbor Town and get all the following quests in your journal (solving a quest will make your decision, so hold that off for now);
1a. The Family Heirloom (Don) (Toni in Merchant Quarter)
1b. Take the Don's Heirloom to Hernandez (Order) (Hernandez, Harbor Guard)
2a. Lukor Wants Five Armor Plates (Don) (Lukor in the Harbor)
2b. Carasco wants the five armor plates (Order) (Carasco, Harbor Warehouse Guard)
3a. Bring the packages back to Weasel (Don) (Weasel near Merchant Quarter)
3b. Evidence for Marcelo (Order) (Marcelo, Merchant Quarter Guard)
4a. Romanov's Seaman Chest (Don) (Romanov the Pirate)
4b Sergio Wants Romanov's Gold (Order) (Sergio, Harbor Guard)
5a. Protection Money From Costa (Don) (Delgado, near back entrance)
5b. Pretending to work for Delgado (Order) (Sebastian, Guard near Delgado)
6a. Doyle Must Disappear (Don) (Cid, at route between Poor Quarter/Harbor)
6b. Get Rid of Cid (Order) (Rodriguez, Harbor Guard)
7. Good things comes in threes (Order)* (Carasco, Harbor Warehouse Guard)
* The Don path cannot be taken until you done four other Don quests. It's name is "Three Golden Bowls for Scordo".
Now make an ultimate save here in case you wish to replay the game and do the other path.
Now you must chose which faction you support. Doing 4 quests for one faction (Don or Order) will make your choice, but you can still do all quests and you can still do 3 quests for the opposing faction if you like. Helping the Don will unlock the path towards becoming a Bandit, helping the Order will unlock the path to become a Mage. Warrior is always available by getting beaten down by the Order when you first reach the Island, or it can be chosen instead of Mage. You can do both 6a and 6b and get +1 for both (tested in v1.10), but if you then get 4 for both factions, the main quests will be canceled for both and you have likely screwed up the game, so keep this in mind so you never get more than 3 in the faction you do not want to play.
Once you done your pick, you probably have a few quests helping people out from the Harbor Town, but besides that you are done. You always get more money/xp for an Order quest if you speak to Carlos afterwards.
3. Check in with the Bandits if you took that route, otherwise go to the Monastery.