I think Magic is far and away the most popular CCG.
Developing a CCG is hard. You need good rules and an interesting environment. You would think though that someone could take another establish CCG and turn it into an online game.
I've always asked, where is there no Warhammer online? I don't mean a MMORPG, just the exact same as the tabletop game. Or Silent Death or Car Wars or a million others...seems odd.
Maybe because the companies that make these products are so set in the "sell cards/miniatures" mindset.
Most CCGs have a limited lifespan, save for Magic. You really need a long-thinking R&D staff that will stick around, careful attention to format and rules, etc. Basically, you need to commit to making that CG a long term money maker by spending loads of cash.
Most popular modern CCGs have just been one facet of an overall marketing push. Pokemon and Yugioh both had TV series, computer games, shit tons of merchandise, toys, etc.
Pokemon was far and away the most popular CCG a few years ago. The play rules and card power were crap, though, according to friends. (One guy who works with the developmentally disabled and plays these things with clients, the other owns a card/collectible store)
Yugioh unseated it, but again the actual gameplay wasn't great.
Magic was something like the fifth or sixth most popular CCG at the time.
Magic Online might not be ideal, but they have many of the right things in place. I can be assured, if I take 8 months off, to come back and my card collection will still be relevant. It might even have gained value. The Magic Online format also assures that Wizards isn't cannabalizing thier cardboard business.
Magic is tops right now, but I'm sure in a year or two there's going to be some mediocre CCG based on a crappy anime or cartoon that will unseat it, for a few years, before burning out.