Well, HGSS-on isn't actually the best format. But it's not about the metagame. Considering we only have cards coming from 4,5 Japanese sets in modified, there are a lot of competitive decks to choose from. There were a lot of formats with only 2-3 viable decks (except for some rogues).
Also, it's not about Donphan and Yanmega. They're powerful cards, but they don't break the format. Actually, most of the best decks don't even play them. And as much as I dislike that card, Donphan is important for the format to keep Zekrom back.
Next one is Pokémon Catcher. That card is broken, no question. It makes many decks unplayable. But looking on the rest of the format, I fear we need the card right now. No more flips on Reversal. How many of you missed top cut at Worlds because of Reversal flips? Guess there are quite some. And if you look at future cards like Mewtwo ex with Gardevoir - that deck would be almost invincible without Catcher.
Now to the lack of skill. That's indeed a problem. But again, it's not about the metagame. Stage 1s, Gothitelle, Megazone, and even Tyran are all more skillful decks than some we had in the past years, like Jumpluff, Kingdra or Machamp. Some special rules and cards cause this issue now, not the decks we play.
Then we have overpowered basics. I absolutely don't like them, but as we see, there are enough other decks that still can compete them. Right now, it's ok, but we'll see how it works when Evolite and all the ex Pokémon are released.
The only real problem is the opening rule. It not only makes the coinflip a lot too important, it also makes donks even more common than in SP and speed deck days. It's obvious that something has to be done about this, but that's not up to TPCi. The old rule with the new Rare Candy nerf would be
perfect, and I really hope that they change it soon. But well, there wasn't any perfect format sind DX-on, and as long as it doesn't destroy the game completely, I'll still play.
None of those instances are tournament ending. In fact, the tournament CONTINUES and the player that got donked has THE REST OF THE TOURNAMENT to get themselves back in and win.
No, he hasn't. Depending on the number of players in an age groups, there are tournaments where you can't get in because not all X-1 make the cut and if you lose first round you've the lowest tiebreaker. If you are in a 31-player-tournament and get donked R1, the tournament is over for you without you even got a chance to play. (And this season, you can't even play for rating after that.) It's rare to happen, but there's no way to deny this. And yes, this is one of the major flaws in the current format.