Depends.
Flemish is easier to make in field and without a jig. It's also the only real option with natural fibers if you go that route, since you can't splice in fibers on an endless loop. However, if if you do the twist the whole length you might get more stretch in your string than endless loop, which can slow speeds down just a bit. However you can negate this by doing a two loop Flemish twist like bjrogg mentioned, which basically leaves the middle relatively untwisted like it is in endless-loop.
On the other hand endless loop has some advantages. If you have a jig, and you know the exact length the string needs to be, endless loop can actually be easier and faster. Not only that, endless loop is the best method as far as speed is concerned, since it has less mass in the loops (flemish twists double the thickness at the spliced loops), and less overall twist which minimizes stretching. These two things: less mass (especially at the tips where it matters most) and less stretch; will lead to faster speeds. However these netter speeds may not be that significant, as I haven't actually seen someone test it out. Maybe I will one day.
So to summarise:
No jig, exact length unkown, and natural fibers, then flemish twist is the way to go.
You have a jig, you know exact length, and you're doing flight shooting, then maybe endless loop should be your choice.