The only side-series Pokémon games I've ever played were Ranger 1 and PMD:GtI. I hated Ranger, the circle-drawing was difficult when the Pokémon I'd be trying to catch would demolish half my energy or more in one blow. Even with cheats for max energy/styler level, I still couldn't beat the first member of the Go-Rock Squad's dual Camerupt in mission 10. I guess it was because I didn't have the right PokéAssists, but that Swampert would flee before I could grab it, and if I just skipped it, I couldn't backtrack and find it again later. Argh, so annoying! The story was rather boring, too, and... Go-Rock Squad!? Really? Even the name Team Rocket sounds more intimidating, and we all know that they're a bunch of epic losers. I've never tried any of the sequels, altho I'm sure they're much better. Guardian Signs looks pretty interesting.
Mystery Dungeon, on the other hand, was and is the single-greatest Pokémon game I have ever played. I'd never played the previous incarnations, and since Gates to Infinity would be the easiest to still find in stock, plus it has all the latest mechanics that tend to make life tons easier versus previous generations, I just jumped right in. The story started off kinda slow, with all the characters getting introduced piece by piece, the groundwork for the plot getting laid down early... And then suddenly, you're catapaulted into the thick of the action, and things just snowball from there! You get betrayed, you get heartbroken, you kick all the bad guys' butts in epic come-from-behind fashion... and then you have to say goodbye. I cried more at the ending credits than any video game has ever made my cry before! Sadly, after the credits roll and you return to the Digital--erm, I mean, Pokémon--world, sure, you get to evolve your heroes, but after that, there's nothing left to do except grind, build Paradise, try to recruit legendaries, and buy DLC.