One of the most difficult problems in learning German is the neuter gender, to which about a third of all the nouns belong. I believe most, if not all romance languages have only a masculine and a feminine gender, which simplifies learning.
Another problem facing English speakers learning German is that one cannot always determine a noun's gender by looking at it. In Russian, which also has three genders, one can almost always determine a noun's gender by its spelling, although "type two" masculine and feminine nouns, which end in a consonant followed by a soft sign--such as the feminine noun "bezopastnost'" ("Security"--the "B" in "KGB")--can sometines pose problems for learners.
I didn't have any problem with three genders as opposed to two. My biggest problem was the strange overlap of articles. Is there any reason why die is used in feminine and plural nominative and accusative, while der is masculine nominative, feminine dative and feminine and plural genitive? Six words are spread over 16 pairings of gender and case with no logic I ever really found. I memorized it for tests, but I never really learned it.
M F N Pl
Nom: der die das die
Acc: den die das die
Dat: dem der dem den
Gen: des der des der