Basically imagine Jak and daxter go back in time to slightly before heaven city was built/founded. There you go through the story of Mar, in a crazy world filled with metal heads and dark eco mutated lurkers (or other enemies from Jak 1)
You join a resistance force in your battles, and i think it would be cool if in the final battle, you and nother fighter take down the final boss together, and afterwards he reveals himself to be named Mar.
Some mechanics i thought would be cool is Jak has ALL his forms of eco. These can be activated on their own, with blue giving a speed and attack speed boost and a jump hieght boost, red giving a melee attack damage increase, and yellow shooting fireballs (and perhaps a fire spray using the spin attack?) Dark eco would activate dark eco mode, where square fires dark blasts, circle is the lock on tornado spins, triangle is invincibility, and he can do a dark bomb with jump square. The Dpad would active each eco type like the guns in jak 2/3. Eco wouldnt be used up unless you actually "used it." (attacked with it, or ran with blue eco, ect)
The resistance force also have created a new/old gun (remember its in the past) where they capture those flying metal heads that lob dark eco, and strap them into the gun, and they fire the dark eco using different gun mods.
There are 2 gun mods, one where you fire it on its own, the other inside a shell.
Now when Jak aquires this gun, he can choose to use his eco through the gun, rather than through his body. This would be toggled similar to in Jak 3 toggling through weapon mods. Yellow eco gun would either fire long rangle blaster shots, and the shell mod would fire a turret that sticks in the ground and fires at enemies.
The red eco gun would be similar to the wave concussor, and the shell mod would be a mine that explodes when enemies come close.
The blue eco gun would be like the needle laser, only single fire and slightly less lock on, and the shell mod would be an electrified disk that bounces around like the beam reflexor.
The dark eco gun would be an energy beam gun, that would lock onto enemies and make them explode after a time, and close enemies would be damaged by the explosion, and the dark eco beam would chain into nearby enemies. The shell mod would be a grenage launcher similar to the plasmite RPG in jak 3.
Lastly, i think it would be cool if daxter, before going back in time, created a precurser glove to channel his precerser abilities (similar to the staff used by the fat otsell in jak 3) so daxter can legitate enemies for jak, activate precurser doors or other technology.
Jaks light eco form can also be used, however he would have his light blast from Jak 1 as the square button, circle does the shield, and triangle slows down time. His flying abilities i think should also be unlimited untill he runs out of light eco.
I hope you like my ideas, feel free to comment and give feedback