This might be cheating as both this movies belong to the same franchise, but I feel they were both made to hit the nostalgia bone for old Pokémon fans and be a new movie for new Pokémon fans. Pokémon: I Choose You is a reimagining of the first season of the anime, and Pokémon: The Origin is an adaption of the Red and Green (or Blue) games.
Pokemon: The Origin - Special is a great (shortish) story about Red - a well known pokemon character. It keeps the intriguing story from the original, by adding intense fights and likeable characters - it feels like the original just without the comedy aspect.
If you like stories that don't feature Ash and want stories featuring the side characters, Pokemon Housoukyoku / Pokemon Chronicles is a great anime that features episodes with Pokemon side characters. Its also got more comedic moments then Origins does.
Both anime follow young protagonists who want to become the best at their fields. In both anime, the protagonists often make new friends and rivals, while battling other characters using monsters that have special abilities. Overall, both anime explore similar themes and have a similar mood.
In both anime, there is a young protagonist who sets up to become the best at his field: Yugi tries to become the best duelist, while Red tries to become the best Pokemon trainer. Also, in both anime, the main character engages in duels with other characters using their monsters: in Yu-Gi-Oh!, the monsters are summoned through cards, while in Pokemon, the monsters are summoned through Poke Balls. Both anime show the adventures of these characters as they make new friends, but also new rivals.
Both originated from old games and give guide lines on how to beat them. They also have their on spin-off of the game. While Druaga only contains one scene where the characters actually play the game, Pokemon follows the game up till the battle with Mewtwo.