I actually find the Greninja vs. Cloud MU to be heavily in Cloud's favor if the person playing Cloud is at all familiar with said MU and knows what to do.
Any Cloud that can attack cancel RAR for BAir's or quick turnaround NAir's out of tilt cancels and stuff isn't going to give you the notion anything he does is 'telegraphed'. The only move he has with startup like this is FAir, which also has a disjointed hitbox the size of a small nation and can have most of its endlag cancelled upon landing, it also has several dunk confirms out of DTilt at side stage at middle %'s on some characters.
When Greninja plays Cloud's game (the neutral game), he loses. When he tries to camp Cloud, he loses. When he puts Cloud in disadvantage, if they aren't true hitstun combos then NAir is gonna make him again, lose. There isn't much favoring the frog in this MU. It doesn't help that a lot of Greninja player's I've been against at locals have always gotten super predictable with their counters, leading to easy read punishes. Even so, the Frog has a hell of a time.
Cloud can easily shut down a lot of his follow ups and combos via good DI and just tossing out an aerial, usually NAir. Cloud is always at an advantage in neutral against the Frog as Cloud's main focus is being a neutral character with heavy follow up pressure in disadvantage via juggling, then has dangerous edge guarding potential (2 framing Greninja's recovery with DAir is quite easy if he goes low, and FAir, BAir and NAir can make middle recovery near impossible, UAir making high recovery outright impossible.. this isn't even accounting for IF Cloud comes offstage, which he absolutely can) to boot. Cloud has some of the best pressure in the game, and he isn't slow. With Limit, his dash is actually the 4th fastest in the game I believe, and his aerial mobility with and without Limit is VERY good. He has both speed AND range, making what Greninja does a lot harder to accomplish in this MU.