This may be a mundane answer, but I prefer when there is only one viable deck in the format. It simply makes testing much easier because I do not have to worry about trying out every single Pokémon deck possibility out there. It allows me to really focus on that one elite deck and perfect it, both in terms of the list and of strategy. Just because everyone else is playing the same Pokémon, it does not necessarily mean the games are going to be boring. You are able to get to know your deck inside and out, which allows you to be confident of your play during almost any game situation.
When there is a plethora of decks to choose from, you are more likely to run into matchup problems during tournaments. This can be unavoidable and is simply luck of the draw. A multitude of different Pokémon deck options usually means that some of those decks will have quite auspicious chances over a specific matchup, while being at a disadvantage versus another. This is the nature of there being several good decks.
I will say however, that I enjoy trying to come up with new decks to take out the top dog. If you can come up with a new idea that no one else has thought of and it succeeds, it is an awesome feeling. It is not an easy task, but it is feasable. Our Nidoqueen deck that won Worlds a few years back is a prime example. When Delta (Raichu/Exeggutor) won Nationals, that was really cool too. You just need to analyze what everyone else is using and find a flaw that you can exploit in those decks.
(This post is a response to this poll. Be sure to vote and take part in the discussion if you have not already.)