Most of Nintendo's games really don't lose anything between console and handheld already, and I think it's clear that ports like Xenoblade illustrate that console titles can make the transition to handhelds without losing anything integral in the process. I understand the concern, but I'm not seeing any kind of big change in their general philosophy.
Hell, this thing is probably launching with Breath of the Wild, which is probably the most complex Zelda game ever.
Well, I'm also thinking from crowding out handheld gaming.
I mean take the DS Zeldas--their fingerprints are all over SS, but they could exist as smaller scale projects that covered Zelda for the handheld but there'd be the main Zelda project on console. Same could be said about aLbW or 3D Land.
Now the question becomes, if you have BotW on the handheld, why do you need the 'junior' Zelda game? Nintendo uses those to test concepts and gain development experience on smaller projects. Are we done with new isometric Zelda titles now? I guess they could continue in the form of Triforce Heroes, where the game clearly accomplishes something different. Nintendo stands to lose a laboratory of sorts, and I sometimes wonder what effect that will have.
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It also is just concern over what makes a game suitable to handheld and suitable to home console are not always in sync.
I'll use a controversial example: Fire Emblem. A lot of people like these games on handhelds but I really do not see the appeal. The levels are long, there is no permanent save state (in most of the games) mid-level, it requires a degree of concentration, etc. When I play it on a handheld, I'm using that handheld as I would a console: sitting at home for an extended time. I don't like suspending only to die when I load the game later, especially in a situation like the end of Fates where the levels are tied together with no permanent save.
To make it more handheld friendly, you'd need things like shorter levels (either by being smaller or easier), no permadeath, saves mid-level, etc. Noticeably, Fire Emblem is trying to toe the line between these values and what I want from Fire Emblem. Now, obviously, handheld is just the way FE is at this point--if true, this rumor changes nothing-- but this is the kind of concern I have and I think you can see its effect on FE pretty clearly.
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So I think this fusion is dubious on two accounts:
1- Disturbing Nintendo's software development approach and rendering certain games meaningless
2- Potentially driving Nintendo towards home style or mobile style only with respect to certain franchises, which could be to their detriment.
But it has obvious benefits:
1- Freeing up Nintendo to make less Zelda, Mario, etc. games and experiment
2- Less software droughts
3- All games can be played anywhere with limited hassle
But again, these have nothing to do with the specifics of the leak.