Not really, you just have longer turns in Magic.
Pokemon's only problem was the coin-flipping it could get into, but those cards weren't usually too great anyway.
I can't speak for how it is now, but during the Neo Genesis era it had a lot of strategy to it. Magic tends/tended to be skewed towards requiring early-game strategies almost exclusively; while Pokemon was like that for the first couple of sets, it didn't take long for them to fix it. And to its credit, it never had a single banned card until the 7th set (and even then it was just one, don't even know when another card was banned, assuming there was a second one.