I just discovered tcgone.net, and it looks pretty decent. The gameplay is automated, and you have the choice of "quickplay" matches (you can create your own deck - or use decks others have created - using any cards you want. They appear to have all the cards (with the exception of a few that were just too difficult to program) from the original base set up to Legendary Treasures released in Nov 2013, so they're only missing XY and Flashfire, which were just released in Feb and May of this year) and/or "career" matches (you start with one pre-made deck, and battle other players to earn currency to buy new cards or booster packs. It's only using the older sets right now, but they have plans to gradually add all of them). You can also play against yourself if you want to just try out decks or get a feel for how it works by creating two accounts and logging in on two different browsers, and you can watch other matches. The gameplay is a bit glitchy, but considering it's free and fully automated, it's not bad.
However, if you're brand new to the game, I do highly suggest heading over to the official online trading game (pokemontcg.com), as they have really good tutorials and a much better interface (though it is a bit of a RAM/processor hog. Make sure you turn off all animations and effects if you've got an older computer, it helps immensely), and you can play totally for free, it will just take longer to build up your collection. I would recommend saving tcgone until you've got a good handle on how to play the game, and then use it to experiment to your heart's content with the vast number of cards available.
The other alternative is the pokemon TCG gameboy game, which you can download as a ROM. It's actually pretty fun, and a really good introduction to the game and to deck building because it doesn't take long to put together a decent collection of cards and it doesn't have an overwhelming number of cards to choose from (although it's good to note that a lot of strategies you'll use for this game aren't really effective once you start playing with the newer cards because of changes like stadium cards and pokemon-EX's, but it's still good for building a solid understanding of the basic gameplay). It can get boring after a while though, because your opponents don't really pose much of a challenge once you've built a good deck and learned how to make your cards work together. It's definitely a lot more fun playing against a real person using actual strategy rather than and "AI" making more or less random decisions. (the "AI" you have the option of playing against in the TCG Online is also much better, and has actually kicked my tail several times, which rarely happens with the TCG rom now)
