Greninja is waaaaay better in this metagame than Infernape is. Protean and base 122 Spe are actually really big deals. Protean is so fantastic because it essentially tosses on a free Choice Band/Specs boost on to all of Greninja's coverage moves, which lets it blow past Pokemon that might otherwise be able to handle them. Just to put this power boost into perspective, a completely uninvested Timid LO Greninja's U-turn is hitting about as hard as a U-turn from a fully invested Jolly LO Infernape. Even though Greninja's bulk isn't great, it can still use Protean defensively to mess with checks and survive weaker hits. For instance, it can do massive damage to Rotom-W with HP Grass and reduce its Volt Switch to ~20% damage, whereas it would otherwise do upwards of ~87%. The extra speed is very important as well because it lets Greninja outspeed a lot of Pokemon that Infernape either loses to or is forced into a speed tie against, namely Latios, Latias, Gengar, Espeon, Thundurus, Terrakion, Keldeo, Starmie, Alakazam, and, of course, Infernape itself. In fact, Greninja outspeeds pretty much the entire unboosted metagame besides Deoxys-S and Mega Alakazam/Manectric.
Infernape, on the other hand, just has a lot of problems. Its offenses are a little better than Greninja's, but that advantage is often negated by the fact that Infernape generally finds itself splitting offensive investment to take advantage of its mixed abilities. It also lacks the substantial power boost to its coverage moves that Greninja gets with Protean, which is one thing that makes Greninja so powerful since it can turn even Hidden Power into a strong coverage move. Above all else, though, Infernape just faces so much competition that it's generally not worth using over something else. As far as "fast Fighting-type that can attack specially and still get past Chansey/Blissey" goes, Keldeo is just such a better choice due to its excellent power, solid bulk, better typing, and lack of a need to split offenses in order to go mixed. On the physical side, Infernape faces a ton of competition from Terrakion as well due to the latter's much greater physical power, excellent neutral coverage between its STABs alone, and (again) better bulk. It also faces a ton of competition as an offensive Fire-type from Pokemon such as Talonflame and the Mega Charizards. Heck, even its abilities as a mixed attacker are often overshadowed by offensive behemoths like Kyurem-B. Meanwhile, nothing really gives Greninja a ton of competition. The only other specially offensive Water-types that come even close to Greninja's offensive prowess are Starmie and Keldeo, the former of which is almost completely overshadowed outside of Rapid Spin and the latter of which is fantastic but still lacks U-turn, Protean, strong Ice coverage, a solid coverage move to help get past Mega Venusaur (even Specs HP Flying can't guarantee a 2HKO on 252/0 MegaSaur without Stealth Rock), or a base 122 Spe stat, each of which are parts of what make Greninja so great.
tl;dr: Greninja is really good, but Infernape is honestly pretty mediocre in this metagame.
Infernape, on the other hand, just has a lot of problems. Its offenses are a little better than Greninja's, but that advantage is often negated by the fact that Infernape generally finds itself splitting offensive investment to take advantage of its mixed abilities. It also lacks the substantial power boost to its coverage moves that Greninja gets with Protean, which is one thing that makes Greninja so powerful since it can turn even Hidden Power into a strong coverage move. Above all else, though, Infernape just faces so much competition that it's generally not worth using over something else. As far as "fast Fighting-type that can attack specially and still get past Chansey/Blissey" goes, Keldeo is just such a better choice due to its excellent power, solid bulk, better typing, and lack of a need to split offenses in order to go mixed. On the physical side, Infernape faces a ton of competition from Terrakion as well due to the latter's much greater physical power, excellent neutral coverage between its STABs alone, and (again) better bulk. It also faces a ton of competition as an offensive Fire-type from Pokemon such as Talonflame and the Mega Charizards. Heck, even its abilities as a mixed attacker are often overshadowed by offensive behemoths like Kyurem-B. Meanwhile, nothing really gives Greninja a ton of competition. The only other specially offensive Water-types that come even close to Greninja's offensive prowess are Starmie and Keldeo, the former of which is almost completely overshadowed outside of Rapid Spin and the latter of which is fantastic but still lacks U-turn, Protean, strong Ice coverage, a solid coverage move to help get past Mega Venusaur (even Specs HP Flying can't guarantee a 2HKO on 252/0 MegaSaur without Stealth Rock), or a base 122 Spe stat, each of which are parts of what make Greninja so great.
tl;dr: Greninja is really good, but Infernape is honestly pretty mediocre in this metagame.
