Ah, yes. This is one of the factors of the Pokémon TCG that makes it the game that it is. Not only because it gives you a choice between a deck that you KNOW will work well, or a deck that might not work as well but is different, but because it adds something completely new to the game. It adds the ability to theorize and have fun with new cards instead of just taking the best things in the new set, finding the most obvious and boring combos with them, and playing them in a tournament where someone else is playing the same exact thing. But when you play with a rogue deck, you have the opportunity to explore a whole other variety of decks and strategies that are out there. I mean, if you really do want to win, then your best bet IS a metagame deck. Although not always reliable, things that have a winning streak are obviously known to do well and to stand up to whatever else makes up the metagame. Some rogues, however, are so good that they eventually become part of a metagame (whether or not that was the intention). On the other side, some rogues don't work out in the end because they AREN'T reliable. Then we begin to wonder... what really MAKES a rogue? Is a rogue a deck made up of cards others don't think are good that sort of works on paper, or is a rogue a deck YOU enjoy playing that doesn't do too well most of the time, but you have fun with? That's up to everyone else I guess, but my personal opinion is that a rogue is something that is unique and special. It's something that only belongs to the person who created the deck, and that person is the one who knows it inside and out. That person, and that deck, are unique because ten thousand people AREN'T playing it like they are metagame decks.
Between the two, metagame decks are generally going to have an advantage over rogue decks. However, the thing about rogues is, no one except the creator of the deck knows how it works. It can completely catch a metagame deck user by surprise, putting them at a disadvantage. They might possibly have to change their strategy to accommodate to a trainer lock or maybe a power lock or spread damage. This could be a problem for them if they can or cannot get around it. There will ALWAYS be viable rogues that come with every set, the trick is finding ones that don't fit in with the metagame before anyone else does. ;D