Actually, pokemon comes out in three different versions, as did the newest megaman games. The only reason they do this though is because they know that more versions just means more money from all the little kids that want these games.
Don't give up on it, trust me. BN3 was my first Battle Network, too, and I also found it pretty difficult. It's probably one of the best in the series though. Even if you find the viruses challenging now, they'll become easier once you start getting used to their attack patterns. Some things to keep in mind are upgrade your folder often, use recovery chips when you get low on health, and take advantage of the elemental strengths/weaknesses.
P.S. In BN 5 and 6 there is a Navi Customizer Program to run automatically, but you have to hold the B button for the rest.
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