The percentage you see at the end is the ratio of good/evil of your playthrough. I used the terminology of the Mass Effect series: paragon = good, renegade = evil. This doesn't necessarily mean that you missed parts of the game, although there are some dialog elements that will be skipped if you lie or when you are mean to NPCs.
All in all, to get 100% you'll need to be honest, finish the picked up side-quests and be nice to people. You can be mean and you can lie of course, the game will not punish you for it: it's your freedom as a player to pick the path you like most.