In the Pokemon Anime, the humans are very cookie cutter characters with little depth in their personality while the Pokemon (DP and BW especially) have more personality and a bit more depth and likability to them.
In the Pokemon Special Manga, the humans have a lot more depth and personality to their characters as well as more likability and development throughout the story while the Pokemon have little to no personality and are basically wild creatures with powers that act on instinct and their Trainers' orders.
In my opinion, both ways on how to depict Pokemon have their ups and downs.
The first method is good in that we can like the Pokemon as characters and not as creatures we use to do battle like in the games. We can enjoy our favorite Pokemon with more character traits that are applied to them and we can even like Pokemon that we didn't before. It's bad when we get too attached to the Pokemon when they evolve, are released or given away. Hell, Dawn's Piplup never evolved since Prinplup would be "ugly" in comparison, according to a director on the show. And Ash's Oshawott seems to be heading down the same path.
The second is good in that it makes more sense: Pokemon are the Animals of the, well, Pokemon world and they're creatures with powers who live in the wild (before being captured) so clearly a lot of them (except human-based Pokemon like Jynx or Gothitelle) wouldn't act like humans but as the wild creatures they're mostly based on. It sorta makes little sense when Pokemon raised in the wild have human-like personalities (at least too much) and act less on instinct. It's bad when they're your favorite Pokemon and you don't like how they're portrayed with little character and as living MacGuffins. It's also bad when the human characters overshadow the Pokemon when the series is called "Pokemon" and we can't get invested in our favorites from the games.
My solution: make both the humans and Pokemon interesting characters but don't humanize the Pokemon too much. Also, use the Pokemon's personalities as ways of developing the human characters more as they are Trainers who have to raise six Pokemon as since they're kids, it can help them mature as they learn from their Pokemon and vice versa. This is present in the Anime and many Manga but isn't emphasized just enough.