I haven't had a whole lot of experience with collectible card games that have been "converted" into video/computer games, but the two experiences I have had, have led me to a theory.
My theory is that collectible cards games (or CCGs for short) that have been adapted into video games are purposefully designed to be bad.
Experience One - Magic: The Gathering on the Playstation One
I bought this game back in the nineties, at which time I was regularly playing MTG with friends. I thought; hey cool, now I can play against the computer to practice when I don't have any real opponents around. I was wrong.
I'm not sure if it was to do with the particular video game craze of the time, but this adaptation was crudely wedged into a rather cumbersome Real-time strategy game engine.
One glaringly obvious example of the problem of trying to fit a turn based card game into RTS clothing, was the use of walls and other defending creatures. In the normal MTG card game, you can choose to apply damage to one of your untapped creatures instead of yourself. In the RTS Playstation version, by not giving your creature an order (i.e "go attack that guy") the creature would idly stand beside you and do nothing as the opponent's creatures advance to attack your wizard.
Experience Two - Yu-Gi-Oh!: Duelists of the Roses on PlayStation 2
I was curious to see how the new school of CCGs compare with good old MTG, but didn't want to suffer the shame of trying to start a game of yu-gi-oh with friends. So I thought trying the latest PS2 version of the game might be a good way to get a feel for the game. Wrong again.
This time the game had been turned into a sort of (console style) RPG and card game hybrid. You choose a deck to start with, then follow a series of paths, playing against certain other characters (and deck types) in turn. Obviously not happy with the standard way of playing yu-gi-oh, the developers allowed the cards to move and terrain modifiers to the game. Neat.
This is where my theory kicks in. If I was to develop a CCG video game, I'd want it to reflect what it's really like to play these games with real people in the real world. Where are the booster packs you can buy from the local store? Where are all the different people (with different decks) who you can challenge? What about becoming good enough to enter a tournament?
The simple answer to my questions: If a CCG video game is developed that is just as much fun, and has all the same elements/mechanics, of playing a CCG in the real world, people will stop buying the real world cards. This equates to loss of income.
By applying this rule, I believe that the game designers are told, "sure make the game good, but it can't be the same as the real card game". And so, bad video games are born.
There is of course an exception to this theory. That is, you make your CCG video game just like the real world, but players must buy their virtual cards with real money. Case in point Magic: The Gathering Online.
This is, of course, a rather cynical and subjective view of the current situation. But I offer the following, my example of a good CCG video game.
You start off with your chosen starter deck. Each week you get an "allowance", which you may spend by buying boosters or individual cards at the virtual comic book store. You can play around with your deck however you please, creating as many combinations of cards as you want. You can then travel to different locations (depending on your current ranking). Perhaps at low levels you can go to the school library, or the local McDonald's or something. As you progress you are allowed to visit more worthy hives of gaming activity: perhaps playing at the comic book store or eventually tournament halls. Once at your chosen location, you can approach the different people there. You could trade cards with these people or challenge them. Of course their playing ability will depend on the place they're playing, and their willingness to accept your challenge will depend on your ranking.
As you progress though the game and your ranking increases, so will your allowance. Giving you opportunity to buy more boosters.
Sure you could have a storyline, but take a page from the Grand Theft Auto book and include "fixed" characters at the different locations, that you can chose to approach when ready, to advance the story.
There could be several other goals in the game. Maybe collecting a complete set of cards, winning a tournament or other acheivements like holding the record for most wins in a row.
This, in my opinion, would be a great video game but, alas, would most likely clash with the current CCG video game sales mentality.
Thanks to user X (sorry, erased your message and can't remember your name) for pointing me in the direction of an older Magic: The Gathering PC game made by Microprose. This is a pretty excellent version of the game that doesn't try to change any of the mechanics.