Okay, I have gone through a trial run with the L333 Thrusters and I have my personal route.
I set my deck with the fastest animation as my main priority:
3 x SR+ Aqua (Icicle Spear), 3 x SR+ Armored Aqua (Magic Pulse), 1 x SR+ Roxas (Ragnarok), 1 x SR+ Sora&Axel (Meteor Rain), 1 x SR+ Sora&Riku (Raging Barrage)
All with Combo Plus, Hybrid III/IV, and Attack IV/V. None with Reflect Guard or Counter.
None of them are boosted so I need 2 turns to kill each thruster. Though it will only take me 1 turn if I boost them all.
Blue Route (12-14 per run):
1) Start from Path to Cliffs in Woodlands, go to the extreme left of the cliff and use the booster. Kill 2 of the 333 that are beside each other, run straight for the 3rd. (3)
2) Go to Tram Crossings and run to the end for 1. Immediately go below to Area 6 for 2 more. (6)
3) World Map again and pick the 2nd option, Area 1. Go to the middle platform for 1 at the top left. Then run back to the rightside map, towards the water area for 2 more at the log. (9)
4) World Map again and use choose Dwarf Cottage. Kill the 2 on the left, go down to Dark Forest for 1 more right in front of you. (12)
5) Head to the normal Daybreak Town and kill the one on the top left. (13)
*My time ran out here, but if you are able to one-shot all of them, or have even faster battle animation:
6) Head to District 2 on the right (not left because the blue one there is too far), kill the one on top of the first flight of stairs. (14)
7) If there is time left, re-enter Daybreak Town and head to the Attic with 1 on the second level. (15)
*If you still have time left after all the above steps, there are 3 more you can consider.
1) After killing 3 at Path to Cliff in step 1, you can head to the left map for 1 more at the entrance.
2) From the middle platform in Mines Area 1, you can go to Area 2 for 1 more at the middle area up the stairs.
3) After defeating the one at the Attic, you can go to the rooftops for 1 more at the very end.
Red Route (12-16 per run):
1) Starting from the left end of Seaside Promenade in the event world, kill the 3 while crossing the bridge. Go down the stairs, head to Seaside Park for 3 more. Or you can start from Seaside Park and head to the Promenade. (6)
2) Go to Desert, Castle Gate Area in Agrabah for 2 at the top. Head right to Caravan Trade Route for 2 more at the top as well. And right again to Wayward Desert for another 3, 1 in the middle 2 at the bottom. (13)
3) Re-enter Desert, Castle Gate Area, head into the Plaza and go to the Desolated Shop on the left for 2 more. (15)
*From this point you have to choose according to your remaining time. If there is time for both, then choose A first. For me, I only have time for 1 so I pick B as map transfer is faster than running that distance.
4A) Leave the shop and run to the right end and enter the Warehouse for 1 more. (16)
4B) Go to Tram Crossings in Woodlands and there is 1 near you. (17)
5) If there is still time left, go to Path to Cliffs in Woodlands, immediately head to the left map and all the way down for 1 more. (18)
*If you still have time left after all the above steps, there is 1 more you can consider.
1) After the Warehouse, head to the rooftops for 1 more at the right end.
Yellow Route (12-13 per run):
1) Start from Morning Dew Forest, Middle Level with 2 on the leaves at the bottom end. (2)
2) Go to world map and select Bizarre Branch Path, kill the one at the top right. Head to White Rabbit's House for 2 more at the top right. (5)
3) Go to Agrabah, Rocky Ground of Rejection and kill 1 at the top and 1 at the bottom. Head left to Faltering Sand Dunes with 1 at the top and 1 at the bottom as well. Left again to Dry Desert with 1 at bottom right and 1 at bottom left. (11)
4) Go to Tram Crossings in Woodlands and kill 1 in the middle. (12)
5) Choose Bizarre Branch Path again, turn small and go left to Morning Dew Forest, Upper Level for 1 more. (13)
*My time ran out here. For those with time left:
6) Go to Dwarf's Cottage and go to the left map for 1 more at the end. (14)
*If you still have time left after all the above steps, there is 1 more you can consider.
1) Go to Path of Cliff in Woodlands, head left and go all the way to the top left for 1 more.
Edit: Corrected an error on the red route thanks to QuintusKing.