I think the only problem with this would be how the gameplay works.
In the perfect world, Ratchet and Jak both control like they do in their respectve games and you'd be able to change between the two on the fly to do some really sweet combos in combat and platforming. But doing that would require completely changing the game's coding every time the player presses a button because of the way each character plays like, and that would probably be very hard to do…
I know what you mean. And I think that they could probably achieve it pretty well.
I think these problems all come from the physics that the games are trying to apply to objects. All games have their own way of doing this, and their own special code. So literally combining 2 games is actually a very tough challenge. The best way to do this is grab the more capable game engine (Ratchet & Clank) and add the Jak and Daxter character, and many remade Jak assets into the game as well.
The art style would need some tweaking, but I think it is very doable.
STORY
Talwyn contacts Ratchet & Clank, and tells them that they've found Nefarious. All they know from intercepting his transmissions, is that he's posing as something called a "Dark Precursor". That's enough to make R&C to grab Qwark and head for the planet where the transmission originated from. An uncharted planet on the fringe of the galaxy, that is home to three factions of creatures: Humans, Lurkers and Hora-Quan (known on this planet as Metal Heads). After being shot down by Metal Heads, they fight through to a peaceful Lurker Village, where they explain themselves to the Head tribesman, who then suggests them to seek out a great mythical warrior called "Orange Lightning" and his sidekick who they forget the name of.
And so they go on, and eventually Jak and Daxter join the team, and they need to stop Nefarious and Errol one more time. As well as this, Samos and Keira help Clank understand the risks of repairing the Demensionator to help Ratchet find the Lombaxes, while the heroes (and Qwark) are working on figuring out more on the history of the Metal Heads and Precursors on a galactic scale. This leads them to discovering several ruined worlds, and finally the real Dark Precursors. Of course Dr. N will not let the real precursors be the final boss.