Completely different. The games, at least XD and Colosseum afaik, are set in Orre, a barren desert region where there are no wild pokemon. All pokemon are assumed to have come from other regions, brought in by trainers. How do you catch pokemon, then? Well, you steal them from other trainers.
There's a reason for this. In Colo, you are a defected member of a criminal organization which has machines that enable you to steal other pokemon. Obviously, you defected in the most dramatic way possible, by bombing their headquarters and escaping on a hoverbike(yes, the protagonist is not a rural 12-year old with dreams). A much larger and much more competent organization, Cipher, is working behind the scenes on shadow pokemon, or pokemon whose emotions are scientifically removed in order to become soulless, powerful machines. You meet some chick who can tell what's shadow and what's not, and you both are on a mission to Snag (catch) these shadow pokemon and restore their emotions, or purify them.
I would go into XD's story but it's pretty much the same.
For some reason, I dreamt that Nintendo decied to betray me (just like Capcom and Square Enix) and turned Pokemon into a FPS. You play as a... Uh, a generic action movie star (with huge shoulder pads and an eyepatch) and your enemies are mutated Pokemon.
Ever seen those "realistic Pokemon" pics? Uhuh, that's what I'm talking about. The heck did I eat yesterday?
Pokemon wasn't supposed to be a villain based anime like DBZ.It gives more priority to various adventures.And I actually like the currant villains (other than Jessie and James),they bring a a bit seriousness to the show.But if they became too much destructive and prioritized, there wud be no difference between Pokemon and DBZ.
One of the things that I like about Pokemon is that it can influence our emotions.Like I still remember the day when I became very depressed after watching the episode where Misty leaves to become the gym Leader of Cerulian city.But u won't find that in DBZ.