I realise this topic is a few days old, but wanted to put in my thoughts:
Pokemon is not like chess, where the best player always wins. There are too many situational factors (pairings, coin flips, misplays, bad draws) that all affect the outcome of the game. These are things you can't control, so when you're preparing for a tournament you have to focus on the things you CAN control, which are namely 1) deck choice and 2) knowledge of matchups from playtesting. If you look at the top 32 at large events, you will often find the same names because these are the players who know all the matchups thoroughly, choose the right deck, predict the metagame correctly, and avoid misplays. I think this explains why "unknown" decks seem to do so well at the first tournament they appear at, and then only enjoy limited success after that - because the person piloting it knows all of the matchups while their opponents know nothing, and are therefore more likely to make misplays or walk into traps simply by not knowing what to expect.
Usually when you're preparing for a tournament, deck choice usually comes down to a combination of what you think you will be facing, and how the deck performs against those matchups. You then tech appropriately based on your metagame. It's a case of balancing the percentages (percentages assuming all other factors being equal because that's all you can account for). For example if you play four of Stadium A you might improve your matchup against archetype X but also decrease your chances against archetype Y, and vice versa if you play Stadium B. But it also depends on how much this effect is, and how prevalent decks X and Y are in your area. What you end up going with will depend on what (you think) the metagame consists of...
The problem with the current format is that this process starts to look a lot less like science and a lot more like a guessing game. Whatever you are playing, you will be taking an autoloss to at least one of the top-tiered decks (and potentially several others, I mean there are like 20+ decks out there =/). And for argument's sake, when I say "autoloss", I mean a matchup that when both decks set up, all other factors being equal, you will win less than 20% of games against. If you want to argue this definition then fine, I'm just pointing out that whether you like it or not, there are matchups for any deck that you will lose the majority of the time, regardless of skill. Anyway, this means that no matter how good you are or what deck you use, all it takes is a couple of unlucky pairings and some retarded draws and all of a sudden you can't make the cut. Compare this to a format where decks don't necessarily hard counter each other, and the better players can make use of tech to improve the unfavourable matchups (which obviously still happens in the current format, but most autolosses can't be eliminated by the addition of a couple of tech cards - if they could then they wouldn't be autolosses).
The spinoff from this is that people will try and play metagaming decks, which autowin against some of the top decks and perform poorly against the rest of the field. I'm talking about the hypothetical guy with the Dustox EX/Ninetales deck (which someone mentioned earlier) who beats a couple of Medis and then ends up 3-4, effectively burying the resistance of the better players who were using Medi. In the same tournament, several other Medi players (even if they're not as good as the other Medi players) won't get paired against this guy, and will easily make the cut. Or in another scenario, the Dustox/Ninetales guy somehow makes the cut - one of the Medis gets paired against him, the other gets paired against a Rocklock. Perhaps Medi was the best choice for the tournament, but OOPS there go your chances. This sort of randomness is something you can't tech against, and I don't think it does much to promote skill =/
From an observer or less skilled player's perspective, a really diverse format like this is awesome because it makes the whole tournament more exciting and interesting, and increases the chances of you scoring wins against superior players. From a skilled player's perspective, it's a metagaming nightmare, especially when you have to win (only first place at NZ Nationals gets trip to Worlds)...