How about these rules:
1. As Danisthirty suggested, all tiles are truly mixed. It could be done in a box, covered by a piece of material, so you don't see which tile you draw.
2. Scoring is done depending on which meeple is present in a feature. For example, if you have islander in a feature, you can take only goods from it, or, if you have a hunter in a "city", then you score 2 points per tile, etc. You can even have more than one follower in a feature, and they will be scored differently!
3. River can flow into the sea. In that case you can also count in all the fish in a sea for a hunter on the river. It can be done also for huts, sea could connect several rivers and will be counted as a lake for hut scoring.
4. The same could be applied for seas: fisherman can take fish with a boat not only from the sea, but also from nearby lakes, and this fish could also be covered by a boat tokens (however, we could quickly run out of tokens).