I have been learning German for a few months, I always thought that I was rubbish at learning languages but I am enjoying it more than I did at school.
The whole thing of masculine/feminine and neuter nouns is a minefield. You have to basically learn the Der/Die/Das with everything- there are sometimes clues but it's all a bit random.
But it's the case system does my head in. 
I love the idea behind the logic, that in itself is very German and organised in a sentence. So that you can tell if an object is the subject or having an action applied to it. But... and this is the but, it only applies to the masculine nouns. So Der goes to Den, but Die stays as Die and Das stays as Das.
So, on the one hand, the Germans are saying this is really important and it means you can have 'fun' with the word order (although you actually can't that much because they have strict rules about that too), but it can't be that important if the majority of the nouns don't change.
And then, when you learn the dative (third case), the Der changes to a Dem, but the Die changes to a Der. Re-using a word! Why couldn't they have a Dez, or a Deg- something to differentiate it from the masculine?
I'm sure there are nuances with English for learners too- I'd like to hear them. What other rules in other languages make you completely baffled?