My Thoughts:
1. First of all, GOOD MOVE. This initial effort is already a Godsend and we haven't even played it.
2. People, don't be spoiled; be patient. I know you're used to videogames hitting the shelves 100% developed, but this is kindof a new thing for Pokemon, so give them time to program, work out the kincs, and stuff. Eventually, they'll probably get the point where you can even play UNlimited on there. But, consider the number of cards, powers, bodies, attacks etc. need to be programmed into that game!
3. DO NOT INCORPORATE INTO RANKING SYSTEM! This shouldn't go into the realm of "Online Sanctioned Events" because the entire educational (and social) value of the game diminshes. In essence, this would just become one more videogame for kids to play in their rooms and get over.
The table card game is interesting and withstands the test of time. It involves social interaction, attention to social mores and courteous behaviors, and encourages mastery of basic math and reading skills.
The videogame can be played in solitude and lacks face-to-face social interaction.
So, the videogame will be Phenomenal for decktesting, but should really be used for decktesting and online fun.
The, live, table card game events, however, should remain the only sanctioned events that affect points, rankings, and invites.
Pokemon TCG should not completely migrate over to videogaming.
4. League Play
Sanctioning Online play would cause me to lose about 90% of my league kids. I think it'd kill the live TCG event altogether. I predict they'll be some residual affects for those who ONLY practice online. If the game is going to perform actions and computations for the user, people may be less likely to 'do the math' and read the cards. This could make face-to-face live matches clumsy.
CONCLUSIONS
Pokemon Online TCG = SO GOOD.
Sanctioned TCG online = not so good.