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PsychicHero
I think many of those combos you're discovering are really good, but they all rely on you reading your opponent. Most of those you mentioned are not true combos, they can be air-dodged or attacked (I always think of Yoshi's Nair, if it could come out at any point, your combo is not true). However, those are all really good things to be practicing. I think Greninja's Up-throw is his best throw by far because it can lead into so many of those follow-ups, all of which are able to beat one escape option or another with a rock-paper-scissors effect. For example, if you up-tilt or up-throw your opponent above you at mid-percent, and they airdodge immediately without jumping, you get a free charged up-smash while they fall back down to you. If they don't airdodge, you get a free short-hop up-air. If they airdodge late, you get a lot of stuff (double-jump nair or dair, full-hop ffalling upair spike, double-jump back-air if you read their DI left or right). Know that all of these are potential follow-ups and never stick to just one because it worked one time. Read your opponent and punish accordingly.
Its time for Hydro Pump
To quickly summarize, Hydro Pump (Greninja's UpB) is godlike. It is similar to Pikachu's UpB (quick-attack) in that it has two separate movements, each of which can be controlled by a different directional input in a cardinal or semi-cardinal direction (North, S, SW, NE etc). It differs from Pikachu's UpB in that Greninja's can travel twice in the SAME (semi)cardinal direction, e.g. HP twice in the up direction, and covers slightly less distance than Quick Attack. However, Hydro Pump ALSO has a secondary effect of using the water that Greninja shoots behind him to push opponents away. I believe the boards have uniformly accepted the term "Hydro Push" to describe this effect. It is also worth noting that each of Greninja's pumps has, at the end of the stream of water, a hitbox that deals a small amount of damage (2%?), which is what enables KOs off the top of the screen if you push your opponent high enough. For the rest of the post, I'll describe "Hydro Pump" simply as "HP", and "Hydro Push" as "HPS".
The uses of this move are countless. It recovers, it KOs, it spaces your opponent away, it deals damage, it helps in camping, it aids mobility, it gimps your opponent, it stalls their options, it has bubble for anti-air (i'll get to that), and its flashy as hell, i love it.
The problems are, it can be risky, you can SD using it, it has a tad too much startup lag for use in CQC, it can get predictable, it falls to better options that Greninja has in a lot of scenarios, 3DS makes it hard to control, and it can be airdodged.
Like I did with Shadow Sneak, I think I'll just talk about when I've found this move to be most effective in high-level play.
1. Gimps
More of you need to learn to gimp with this move. I can't even tell you how many KOs HPS has earned me, and in a game that no longer has edge-hogging and gimps are increasingly more rare, this move is a godsend. HPS outright destroys the UpB recovery of the following characters: Ness, Ike, Shulk, Kirby, Lilmac, PacMan. For any other character, UNLESS they use a recovery move and immediately snap to the ledge, they can be put into free-fall and HPS can knock them away from the stage to their demise. This works on everyone EXCEPT: Yoshi, BowserJR, G&W, DK, Lucario (sorta), Villager (sorta), Olimar (sorta), Megaman and Sonic. Most of these resist HPS because their UpB allows them to keep doing moves, which can interrupt you or enable them to recover in other ways anyway. The "sorta" characters are able to avoid HPS most of the time, and if they get hit, can most of the time still recover. If you connect perfectly, however, they will still die. The basic recipe for a HPS gimp KO is to wait at the edge for your recently-launched opponent to use a move to recover. Either hop offstage with them and use HP to get yourself back, shooting water at them in the process, or wait at the edge of the stage and do a single HPS away from the edge with perfect timing to catch their recovery as they use it. Enjoy the free stock and fill your shurikens with your opponent's tears.
2. KO
Launch your opponent above and away from the stage with an attack. Chase them into the upper corners close to the blast zone. Use your first burst of HP to get even higher and closer to them in the corner. This will usually elicit an airdodge from your opponent if they haven't done so already. Use your second burst to HPS them into the upper blast zone, where your hitbox will KO them. THE ONLY WAYS FOR YOUR OPPONENT TO SURVIVE THIS ARE WITH AIRDODGE OR MOMENTUM CANCEL OF SOME KIND...or if you just miss. If you connect with HPS and they're high enough, they will die. The reason this became a habit of mine is because it is almost 100% safe. Your second burst of HP will always be pointed up, meaning Greninja will be sent down. While your opponent is busy either dying or trying to dodge HPS, you will already be on your way back to the stage. Unless they are able to hit you between your two bursts of HP (unlikely, you shouldn't be THAT close), you'll be fine. It has never happened to me.
3. Recovery
Obviously, this is what the move was meant for, but it is far more complex at high level than just "UpB to the ledge". That may always be your safest option, and it is a very good one, but sometimes your opponent will try very hard to cover it so you will have to get more creative to recovery safely. The first alternative that comes to mind is to recover over the stage. Usually, this is a no-no, but with HPS, it becomes completely viable. If your opponent is standing at the edge and waiting to guard you, and their offstage game makes you question the option of recovering low, then RECOVER THROUGH THEM. This may only trick your opponent once, but that may be all you need to win the set. You HP into your opponent or above and past them, and your second HP should push them away as you land, making it NEARLY IMPOSSIBLE TO PUNISH. Use the angles available to your HP to mix up this option, and use the second HP to mix up where you land. Imo, SS is still a safer recovery option, but it requires more forward-thinking. If you didn't start charging SS while you were recovering, HP over the stage could be your safest last-second option (assuming the ledge is unsafe).
4. Bubble
I haven't found a consistently reliable scenario in which to use this, but I'll explain it first and maybe you guys can help me find one. If Greninja is on the ground, you can use HP, but not twice unless the first one is into the air. In other words, you can't HP on the ground forward and then again backwards without your feet leaving the stage. You can, however, HP away once and stay grounded. Another option is to use Bubble, which won't send you far away like a single HP would. To do this, input UpB and then any variation of the direction "down" immediately afterwards. Greninja will always turn to face towards the direction you sent the bubble if he wasn't already, and only travel a small distance across the floor. Taking 90 degrees to be straight up, there are 7 approximate directions to send a bubble: 25°, 45°, 65°, 90° (up), and then around the opposite way aka -65°, -45°, -25°. If you try to bubble at 0° in either direction (right/left aka East West) you will do the single HP away that I mentioned before. To clarify, all of this is only possible with a single UpB input from the ground aimed DOWN (plus an angle). Please help me find a use for this, its awesome. So far, its only a decent anti-air move to be used defensively. The range on Bubble is the only thing that even makes it worth it. Without that, there is probably a better option for Greninja to do every time.
There's honestly a ton of other uses for this move, but they're very situational. If anything, the reason I'm posting this is because I think there is more to be discovered and I want to encourage all of you to employ HP and HPS heavily and diversely into your arsenal if you haven't already. Only then can we find out everything it can do.
TL;DR: Use Hydro Pump a lot, its amazing.