I agree with you that the deck has some shortcomings with some of the combinations that you can draw but most of the decks in standard are at least a little clunky. Kevin Baxter wrote an article on another website that goes into his strategy of how to best play this deck. He also went into the details of what sequence to play your various item cards and what to battle compressor depending on the matchup. The power of the deck is the versatility against most of the meta decks.. For example, Against Manectric, you will likely need to get out Gallade (twice) and try not to to bench Yveltal EX until the end of the game for a final knockout, vs. Night March you must focus on using Baby Yveltal and Zoroark with Gallade to draw what you need and will need super rod to win; try not to bench or discard EX's including Shaymin since most NM decks play target whistle and puzzle of time. There is space in the deck to include cards that help you in whatever match ups you expect to see most but agree with you that Max Elixir is not a good card for this deck. If you are having a tough time getting out Gallade when you really need to, recommend testing 1 copy of Unown and 3-4 copies of Puzzle of time to help consistency and flexibility.The difference between Max Elixir and Dark Patch is that Dark Patch still accelerates from the discard, whereas Max Elixir accelerates from the deck. Dark Patch doesn't contradict Yveltal at all - in fact it helps it out. You aren't pressured to keep using your attack for energy acceleration, so you can focus on stronger hits. It also synergises much better with Battle Compressor. Max Elixir creates a strange disconnect where you want a lot of energy in both the deck AND the discard pile, which splits your attention too much. You don't want to dump energy with Battle Compressor because you then drastically cut your odds of pulling off Max Elixir... but without dumping them you can't really accelerate with Yveltal.
Having done some testing with a turbo Yveltal deck (using a similar engine to the Palkia and Gardevoir decks I've been trying out), this disconnect is a bigger deal than you might think. You typically end up trying to focus too much on either Yveltal or Max Elixir. If you accelerate with Max Elixir, you have to draw them first, and you probably won't dump enough energy to reliably use Yveltal. But if you focus on Yveltal, any Max Elixir's you draw are likely to come up dead. The way around this would be to play more basic darks, but then you probably don't have the space to play DCE... since Max Elixir tends to be most reliable when you play 12-13 basic energy.
I'm sure a smarter player than me could make it work a lot better, maybe with more judicious use of Battle Compressor to thin the deck out better for Max Elixir. I don't think YZG decks run nearly enough darks to run Elixir's efficiently though (the standard is 7-8, right?).
So anyhow... I've given this deck an honest go on PTCGO, but I gotta ask: how do people actually play this deck? I'm using a list that was on one of the front page articles at one point, and it just feels so awkward and weird to use. I keep drawing these bizarre hands that are really difficult/impossible to reduce down to play Maxie's, and often end up in dead draw situations cause I can't play enough Supporters or something. I know every deck has their dead moments, but even with a proven list I just couldn't get this deck fired up properly. I dunno! I'd ask what am I doing wrong, but since I don't have any demonstration of my playing with it I think the better question is what's the best way to look at playing the deck? Like what early-game plays should I be looking for etc. Clearly I am doing something wrong with the deck, but I don't know what.