Is building a stroked 318 better than a stroked 340/360?

That depends on whether you will run carb or EFI. Yes there is the injected 5.9l but a fair number of the carb versions around also.
The Gen 3 is injected with DoD and variable cam timing. Those two are trouble spots and should be deleted. Then if you want a carb, you need an ignition controller for sparks. Once you choose EFI you need to be proficient with electronics and wiring. There are kits out there, but will add cost.

I disagree with VVT being deleted, it adds a fair bit to the motor. And honestly, I think a carb’ed G3 is a waste of time. Not that there aren’t advantages even with a carb and deleting VVT, just that the EFI and VVT are significant advances. Maybe it makes sense on a race motor, but in my opinion not for a street motor.

Deleting MDS I agree with, just not enough of an advantage and anything but the OEM auto would need it removed anyway.

BTW, the only ignition module available for a carb’ed G3 is for the pre-Eagle 5.7 and the 6.1. Later G3’s like the 6.4 can’t be run on them, at least not without changing the crank tone ring. Maybe a megasquirt setup could be built, but the MSD controller can’t read the later tone ring. And they are like $800 after you add the harness you have to buy separate.