I don't believe you're using the right logic here. Not trying to be rude, just trying to give some advice on how I personally think you can analyze the plot patterns better. It's hard to explain what I mean in words but my mind just doesn't want to let this thing go for some reason.
I basically think you're looking at a completly different pattern that isn't connected to the plot. Yes, in order for future games to capture that true feeling of Suikoden it should somehow resemble the plot of previous storys, however, it shouldn't be connected to what order the previous games were released in. That's not a pattern of the plot, it's a pattern of what numbers the games have.
E.g "If S2 and S4 had the same themes then S6 also needs these", or "If S1/S4 and S2/S5 are connected, this might mean there's gonna be a connection between S3/S6".
It doesn't make sense for the developers to keep such patterns in mind while making a new game. What you on the other hand actually can expect them to do is stay true to the continuity and major themes that seperate this series from other JRPGs out there.
And about the "best friend" characters, while we clearly do see a pattern about the protagonists' best friends either dying or betraying the hero this is connected, not only to the the plot, but also to the pattern of what relationships the character-archetypes (in this case the Stars of Destiny) have with each other.
SIII proved that not every game needs a Tenkai star as the protagonist, SIII thereby allowed it's three leads to have different kinds of friends that don't necessarily effect the plot in the same way that previous characters have done before them.
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