I made a very similar thread for the Wii Fit Trainer right after her reveal since so many people were confused as to why she got into Smash:
http://smashboards.com/threads/wii-...n-proves-how-clever-sakurai-really-is.337293/
Since a lot of people seem to be confused about Greninja's inclusion I feel compelled to do the same. Keep in mind this is all coming from a lifetime Pokemon fan who heavily followed Pokemon X/Y all the way up to its release and would much rather have seen Zoroark instead. I'm going to sum this up in 3 quick paragraphs.
So why DID Greninja get into Smash Bros?
REASON #1 - The Pokemon series needed a new, shiny representative for it's latest iteration: Generation 6
This should be pretty self explanatory. With every new Smash game the Pokemon series receives a newcomer to literally "represent" the newest generation. Smash 64 started with Pikachu and Jiggs from Gen 1, Melee gave us Pichu from Gen 2, Brawl gave us Lucario from Gen 4, and now we have Greninja from Gen 6. Thanks to this trend quite a few very popular and viable Smash candidates have missed out, such as Blazekin (Gen 3), Genesect (Gen 5), and Zoroark (Gen 5)... All mostly due to bad timing. With Pokemon X/Y having been released just 6 months ago the timing was perfect for a Gen 6 rep to take the stage. So since Smash 4 continued the trend, why was Greninja chosen over the rest? This leads to my next point...
REASON #2 - Greninja (although still relatively new) is VERY popular among the Pokemon crowd, and has always been treated as the "next big thing" even before his Smash debt.
From the moment Greninja was first leaked he was easily the most popular Generation 6 starter among the fans. Here is a poll that started all the way back in October of last year:
http://www.serebiiforums.com/showthread.php?617734-Starters-Discussion-Thread-v2 As more time went on his popularity only grew from there for 2 main reasons:
1) He ended up being better (in terms of battling) than most other Generation 6 Pokemon mostly due to his stats and special ability... Very much like Lucario.
2) Ash Ketchum, star of the Pokemon cartoon series, ended up choosing Froakie (the 1st stage of Greninja's evolution line) as his very first Gen 6 Pokemon.
Sure Greninja still isn't near the point where Charizard, Lucario, or Mewtwo are at, but you have to remember that Pokemon X/Y has only been out for SIX months. He hasn't had the time the other 3 have had to establish himself. His popularity will only rise once Ash evolves his Froakie, and being a Smash Bro will help as well. He is the next big thing now whether we want to admit it or not.
REASON #3 - Sakurai LOVES thinking outside of the box and surprising us.
This is also self explanatory. He did it with the Villager, he did it with Wii Fit Trainer, he did it with Rosalina and Luma, so is it REALLY that surprising that he did it once again with Greninja? It shouldn't be. Sakurai seems to really have a knack for taking characters that aren't as expected and molding them into fighters that fit well into the Smash universe. Like I said back in June 2013 after WFT's reveal:
I don't think Sakurai was trying to cater to a specific demographic per say. Instead I think he wanted to show everyone that he's still thinking outside of the box with this new roster, so expect the unexpected.
Hopefully this answers any questions some might have had when it comes to the ninja frog. Since he's still relatively new a lot of people are skeptical but I'm pretty sure everyone will eventually warm up to him just like all of the other characters. I'm already starting to.