Like I say, you simply see Snake as character that can be removed even if his kit or work behind means nothing when in reality it has taken a lot from Sakurai and the development team to create, and not bringing him again in the next installment would make all that work to waste. I can tell you right now that at least the moveset of Snake is by far one of the most complex and yet rewarding when played right, I can assure you that Lucas and Lucario by far those two dosen't have or will have as close as something as what Snake has in moveset and I will risk to say that not even a single character from Nintendo could bring to the table for now, what Snake brings in game design wise and game development to Smash.
I did never put on question the popularity of Lucas or even Lucario. I ask you what they can bring different than a character like Snake, Lucas with Ness both hold the series together and its fine but if you tell me, who game wise as a moveset is more different Lucas/Ness/Snake? The obvious answer Snake, he brings another whole moveset, when the other two characters hold some similarities.
A lot of people from smash community will lose a lot more if Snake is cut than Lucas. Snake brings more things to the game than Lucas, gameplay, game design, game development and even fanbase, so yeah I will cut Lucas first than Snake (especially if Erathbound/Mother has a representation in Ness).
I don´t know why you put in a pedestal Earhbound and say that hold a far more precious place than Metal Gear? But here is the catch I´m not talking about series here, I´m talking about characters and what they can bring each and so far Snake brings more than Lucas, sorry but is the truth.
Because I didn´t cut Lucario over Snake, thats your assumption, to tell you the truth I cut Lucario for Mewtwo so if you need to blame someone it should be Mewtwo, by the way if you are so focused that I cut Snake over Lucario, I will tell you that I would prefer to give the fifth character slot to a Mario representative first than the Pokemon series. And you can say whatever you want for popularity but again Snake brings more as character with his gameplay than Lucario.
Your other question is irrelevant if Sakurai thinks is so much work to bring a character like Snake and Sonic, why did he bring Mega Man a character from Capcom, if he is doing again the work to bring some third party characters I would think he will do it again, especially if say character brings his unique mix and color to the roster and half of the work is done, so the resources from the last game could be spent well again (especially Snake, you don´t know how much work Sakurai did put in Snake, I can assure you that is not something as easy to cut as you think).
For your question about Konami and the relationship with Nintendo is simple marketing, very basic, do you think the install base for 3DS or Wii is the same for people that bought a PSP or a PS3? The answer is NO, I would tell you with cars instead, the people that are using 3DS and Wii are the people that like Mini Coppers and Smarts, small cars, with great design and very friendly design, the people that own a PS3 and PSP are people that like elegance, power and luxury like Z350, TT or even a Jaguar, and you sell Longines watches, who will be the people that would buy your watches? and if you have advertising budget who will go towards? The people that own Mini Copper´s or the people that own Jaguar´s.
Is simple as that, the Wii and 3DS will probably never sell as many as copies of Metal Gear Solid as the PSP or PS3 counterparts because of the different segments and Nintendo can´t make Konami change his philosophy and business plans from one day to another so Metal Gear Solid will be in Nintendo platforms even if they flop.
And you can counter thats the reason Snake should not be in Smash because is not even for the segment of people that are owners of Nintendo consoles but you are forgetting something we are not talking about series here, we are talking about characters and Snake once he is in Smash he is treated completely different for the simple reason that is not his games, he is another character that is there to give different flavor to the Smash Universe like Mario or even Jigglypuff.
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