I think I'm now qualified to weigh in on this. When I first posted this I didn't really know anything at all about either series, but over the last two years or so played a lot of these games.
Ratchet and Clank: Hands down the better series. I started playing whatever the free game I got with the Dual Shock 3 I mentioned earlier and once I got into it I got into it hard. Ended up tracking down the other PS3 entries in the series and then the HD Collection of the PS2 games. This is now one of my favorite franchises and the new game is what will sell me a PS4 - I like the series that much. Each game has a bit of a unique feel to it, with each having a "gimmick" to keep things fresh and a load of new, crazy weapons along with the old standby favorites. The level design is great, and there's a lot to see and do. Fuck, I might go back and new game+ all the PS3 games. The HD trilogy was really fun and it was really interesting to watch the progression of the series from clunky and awkward to just pure awesome.
Jak and Daxter: The first game was great. Cool throw back to platformers, just generally a lot of fun. And then I don't know what the fuck happened. Jak 2 is like "Poochie: The Game". The attitude injection is kind of funny more than anything - all of a sudden Jak can talk, sure, I guess....but he's a badass...alright, it was a weird growth period for videogames. But the GTA style of the world feels like it was thrown together in about 3 minutes. Fucking terrible. I stopped playing this in about an hour - I just could not handle it.
Jak 3 seems a lot better, if only because it's an interesting medium between the two earlier games - a little bit brighter in colour, a little bit lighter in tone. I actually had no intention of playing through it but the pacing in this game is so fucking good that I can't stop. I just kind of wanted to laugh at the first little bit of it and all of a sudden I'm probably pretty close to about half way through because every single mission is different, entertaining, and has a hook. Beyond that, it's interesting to see the progression of Naughty Dog, and Jak 3 really kind of tells the story. This is the series that really brought them from Crash Bandicoot (Jak 1) to Uncharted (Jak 3). Just ignore the terrible middle part.
So yeah, in summary: Ratchet and Clank is way better but Jak has it's moments.
