I know the feeling, I was almost in the same boat as you, minus the Magic.
Ok. Well I'll try to explain the basis
After WOTC dropped the card game, PUSA took over (Pokemon USA). They first started with the Ex Series, which goes on for about 4 years but they're outdated. The current formant is the Diamond and Pearl Cards. So that means you can't use any cards from the WOTC series and the Ex series (although energies, Potion's, Switch's, Energy Search's and a few other cards are still allowed)
The absolute basics are still the same, there are only a few small changes, mostly to make the game more efficient.
Darkness and Metal are now Basic Energies, mostly due to there being more of each. This means you can have more then 4 of those types of energy.
Another gameplay change is the seperation of Trainers, Supporters and Stadiums. Supporters are cards that are attached to your Pokemon for a turn and do an effect, similar to a Pokemon Tool but are discarded at the end of your turn. Stadiums are the same as they were in Gym Heroes and Gym Challenge. Supporters are perhaps the most crucial cards in a deck, as they usually involve searching a deck which is extremely useful.
Another change is the reduction of the effects of Weakness and Resistance. Now, Weakness may do 10,20,30 or 40 extra damage, insted of double (although a few cards, mostly legendaries still have this double damage weakness). Resistance is also different, I think it only does 20 less.
If you've been out of it a while, there's also Poke-Power and Poke-Body changes. Poke-Powers are optional, you don't have to use them while Poke-Bodies are in effect unless it says it isn't.
The next change is the introduction of Lv.X cards. These cards are like ultra rare and powerful cards. These are placed on top of your Pokemon and act like a really big powerup insted of an Evolution. The big thing about them is that you can use any attack from any stage of the Pokemon, so it's sort of like the trainer Recall from Gym Challenge.
EDIT: I forgot to mention there's also a new Status Condition: Burned. This is similar to Confusion and you must flip a coin Between turns. If tails, you put 2 damage counters on your Pokemon. Confusion is the same as last time, except its 3 damage counters if its tails.
There are other small changes to gameplay, such as the person who goes first can't use any trainers, but I'm not totally aware of all of these.
I may have missed some other things, but I'm still getting used to the new system. If you have any questions, just ask.
