Why isn't Yu-Gi-Oh as popular as Pokemon?

Because Pokemon is just better organised

In Yu-Gi-Oh

• We have 2 separate metas: OCG and TCG which limit the use of different cards.
• They also give out different rulings for the same cards which can be confusing, even though when we do a world’s championship they always use OCG rulings.
• Cards are releases 2–3 months ahead in the OCG compared to the TCG so there are very different card pools in each. Then the TCG also has a few exclusive cards that further muddy the pools.
• while the OCG does a decent job of getting out banlist in a timely fashion every 3 months, the TCG does it “whenever” so we almost went 5 months without a new banlist. (for those who don’t understand how the banlist works in Yu-Gi-Oh, after about 2–4 week it becomes clear what deck is “the best deck” so we need frequent Banlist to prevent the game from going stale and allow for other decks to be playable).

Compared to Pokemon it’s a mess

Also Yu-Gi-Oh does does not allow cash prizes for tournaments, even at the world's stage.

This really hurts the perception of Yu-Gi-Oh since the most you can win are some mats and some pretty cards (that are illegal to actually play). It’s sorta ridiculous when you think about it.

Pokemon basically has the equivalent of Yu-Gi-Oh prizes as entry gifts.

Then Yu-Gi-Oh has a much, much steeper learning curve. We have so many different types of decks, summoning mechanics and rulings that it’s just ridiculous.

I will bet no card game would come close and if you beg to differ, show me 3000 words guides that do not even begin to completely cover 1/8 of the game.

It is just too hard to get someone into the game since there is just too much to know to start playing so there is only so much the community can grow and there is a lot of burn out from the complexity.

Finally, Yu-Gi-Oh is just too expensive.

In pokemon decks cost about $200 and you can sometimes get away with $100 and do pretty well.

But Yu-Gi-Oh? No, no, no. Decks in Yu-Gi-Oh cost $400-$500. We’ve had formats that had decks that crossed the $1000 marker before. Individual cards can be worth $80-$100.

Source: Quora.com
Credit to: Shane Neary