I think this question can be answered by two different factors, Pokemon's target market audience versus gaming hardware capabilities.
The pokemon franchise can make a much larger amount of money based on creating games specifically for smart phones. There is a humongous number of people who love pokemon in general, the only problem with applying to that fan base is convincing that fan base to go out of their way to buy an expensive piece of hardware combined with an expensive piece of software that can only be used for one focal purpose which is gaming. Sure this fan base enjoy playing pokemon games in general, but the frustration of having to constantly update their gaming consoles and game software specifically for playing a pokemon game that doesn't do much else will easily have it's fan base questioning whether they have the time and money to be able to spend on a game.
When you design a game on a smart phone, it has an easier rate of acceptance by its target audience because the game is designed on a multimedia phone device which people actually depend on because we are constantly using our phones for important purposes other than entertainment. Our phones play an important role in our lives on a regular basis, and thus it is incredibly hard to find a person who does not have a smart phone.
Obviously because of this, it is easy to market a video game on a platform that a huge number of the population is constantly using whether or not gaming was the original intention of the device or not.
For the purpose of pokemon, Pokemon GO has the ability to convince an audience of pokemon fans that are adverse to spending a large amount of money on a game hobby that they may only play once in a while for a few hours of fun, into instead investing their time in a free game that doesn't require any large purchases and also still has enough of the original intent behind the pokemon franchise to keep a grasp on those fans that have otherwise drifted away from the interest of playing pokemon.
This all says to me, that in the end, making pokemon, free to play, smart phone games, is practically like printing money for Nintendo, it is able to attract a humongous audience, and there will always be people who will purchase in game features for the purpose of getting ahead of others within the game. So I really do think making smart phone games will be a new continuing trend for Nintendo.
However, the second important piece of this whole speculation is Hardware capability.
The 3DS and it's kin are designed for gaming. It is a multimedia entertainment device that was built for the purpose of pushing its hardware to the limit specifically for giving the audience a set of spectacular gaming experiences. Smart phones are in fact multimedia devices, but their variety of uses and purposes are so spread out to apply to our daily lives and more adept for communication purposes over all, generally gaming is more of an afterthought to any one single smart phone's design. It's not very likely that many smart phones are ever going to be specifically designed for the purpose of playing high quality games, which means that legitimate gaming hardware will always have a significant presence towards the core audience that Nintendo has acquired over the decades.
I think it is very likely that pokemon games on smart phones will become a continuing trend and I think that it will also rake in a ton of dough for Nintendo, but I don't think that either format will completely dominate one over another. If anything it really kind of separates the target audiences into a casual group and a core group, where the casual group loves pokemon but are not interested in spending their money in copious amounts to own a main franchise game, but instead would much rather enjoy a taste of pokemon within a series of minor transactions across their own comfort zone of appropriate spending. Where as the core pokemon players would much rather enjoy a complete full game where they know that the software is completely dedicated towards their gaming experience with depth and good graphics.
Pokemon games on the phone are probably easy money for Nintendo, and although the audience for the phone games may not be as dedicated to the franchise as the core group of pokemon fans, the point is that the smart phone audience is much larger and much more diverse which creates a larger turn over rate for fandom as well as has a higher likelihood of making more money since the game doesn't require dedication to any one particular gaming console.
...sorry I do go on forever don't I... lol
