I don't think that Splash energy is bad in the deck, however I don't think that you'll make use of it that much since you can't discard it for a GWS and since most of the times you'll want to return it to your hand for the extra damage from moonlight slash.
The most vital stage of the game for Greninja is when you're setting up your Frogadiers.
First of all, it has to be ASAP. (so best case scenario to make your day: you go second with a water energy and a Wally in hand).
Then, if you have more than 1 Frogadier prized (once I had 3) you're pretty much done.
After this point, if you have 3 or 2 Frogadiers on your bench and you're running enough Dive balls/Ultra balls, you'll be able to have 2-3 Greninjas out.
You'll also have to run 2xSuper Rod as your frogs die pretty easy until they go Break.
I have won vs mMewtwo decks even when they had Garbodor out by making smart use of my stadiums (Faded town mostly) and Bursting Balloons but for that to happen you need at least 3 Greninjas out ASAP, then it can be pretty easy.
Really, between the Bursting Balloons and the Giant Water Shurikens (and regular Shurikens if you play Expanded), Greninja only really needs two fully functional BREAKs on the field to clean up the game. Having more than one Frogadier prized can make the process rather messy like you said, but if you're running Splash Energy and can keep it on, that will probably be a saving grace in the long-run.
If we want to be realistic about Greninja's standing in the meta, how high it is depends entirely on how willing people are to cope with abilities. Even in Standard, I can see a Greninja deck making it to Top Cut simply because few people felt a burning need to run Garbodor or multiple Hex Maniacs, and like you said, even after total ability lock, Greninja has other means of chipping away at the opponent.
Anyways, on a personal note, I would say that Greninja BREAK is perfectly fine staying at Tier 2. Its abilities and the durability of its BREAK allow it to overwhelm many opponents, but with reliable tool removal gone in Standard, its too easy for it to get caught in its own head as well as Garbodor's clutches. If we were to get reliable tool removal in the future, then Greninja would easily be worthy of occupying the Tier 1 bracket.