I would say part of the problem Konami has with Suikoden is that they honestly don't know how they would go about marketing it. I mean, when they released suikoden 4 for example, the top most feature listed on the box was, you could build a ship and fill it with mini-games!! OH MY GOD MINIGAMES!!!! You know there's a problem if your marketing begins by suggesting the player recommend is play a different game. In fairness, part of the issue is design of the suikoden games. Here are some thoughts on possible solutions that could be implemented:
Suikoden has 3 modes of combat: standard, duel, and war. This is a pretty unique approach. Out of these 3 though, only the standard battle system has been consistently solid. To date, the Suikoden team hasn't be willing to embrace making 3 solid combat systems. If one is going to market having them, they need to be comparably good to leaders in those types of games. Perhaps duals become more like 1 v. 1 ATB type battles similar in feel maybe to final fantasy 13, maybe war battles take on a feel similar to dawn of war. The more one can integrate the 108 successfully into 3 different combat systems, and make each combat system fun on it's own, the better. Obviously, the main feature of suikoden has been it being a turn based game and I think it should stay so, but the fact is that you need to at least create the appearance of things are happening even if nothing is. We don't have a gaming meta where players want to see their hero standing around nonchalantly waiting for their turn as a bar fills up.
another way to improve gamer enjoyment is to give the player as much control as possible, while remaining user friendly. One of the biggest enjoyment flaws of suikoden 3 was that the player had very little control over the battles. Control however doesn't mean I need this to be an action RPG, but having a large amount of freedom when it comes to things like skills, equipment, combo's and runes, gives the player things to do and invest time into, and especially if you can see the effect(you know you change armor, the armor looks different) the better. Imagine if for example, a accessory you could equip on characters was a banner, that would maybe provide a small bonus in standard battles, and also a giant bonus in war battles, and looked completely awesome on the character's back, and then let's say there is a rallying skill that makes some character's get more bonuses out of the banner. As a player, I now have a lot of input into a character, and I'm seeing that investment paying off.
Making a headquarters: This is something else that should be pretty easy to market, but unfortunately, hasn't really yet been utilized to the fullest extent mechanically. Seems really simple to improve. You have an architect star of destiny, and at some point in the plot you get a piece of land or whatever to build/strengthen your home base. When stars of destiny join who might build a shop, or provide some kind of service/mini game, you see architect and go into a build mode, preferably with a fair amount of freedom to move things around, and you know, as you get X number of stars, the architect can come up with options for expanding the whole thing. Can easily make headquarters building a fun and rewarding part of the game. Perhaps your headquarters even generates its own economy, and one can spend potch to invest in that economy in some way, such as building improvements. Likewise, spending time on one's HQ could provide a combat benefit, particularly in war battles.
Runes: besides the collecting of 108 stars, the true runes are the key plot point of the suikoden series, and yet, you really don't see much of them in the games. While it might be nice to have at least some options with regards to choosing spells, I think more importantly, one needs to see runes in different situations. Suikoden 4 and 5 played around with a tiny bit, but you still don't see runes being used everywhere and anywhere, and for any sort of odd purpose. Presumably they should have a whole host of utility functions that simply haven't been explored. The more the designers explore, the richer the world is, and the easier it is to market the rich and full world the character's are immersed in.
108 stars: obviously meant to be the biggest unique feature. The success of Game of Thrones makes it clear that there is an audience for a fantasy genre narrative with a large host of characters. The important thing is that all 108 characters need to really be fleshed out, even more importantly, the villains need to be fleshed out. There should be characters that you shouldn't know whether or not they are going to end up being a star of destiny or a villain. There should be lots of rich NPC's that fill the world and provide a rich atmosphere. The 108 stars of destiny should have reasonable motivations for being in the stars of destiny, and they should continue to develop once they join, and one of the most enjoyable experiences for a player should be getting to know all the stars of destiny. The game should feel rich and full of characters, not cluttered with them.
summary: if Konami is going to make a suikoden 6, they need to provide their development team with the resources to make the game well. The fact is, Suikoden 6 should be a game that takes 72 hours to complete, and be enjoyable for many more without resorting to gimmicks like mini-games (a few is fine) or new game+ to replace actual content. That takes a large design team and time and money to do well. If they want to market it well, they need to understand it's strengths as a game: a rich world, with interesting characters, and a gripping story, combined with immersive player control and interaction with the world, the characters, and the story.