The differences are generally minor, but can vary with the bow, how well (or poorly) either is made, etc. If you get a "substantial" difference in speed...well, I guess we would first have to decide what a "sustantial" is. 2-3 fps? 10-15 fps? If it's 2-3, then I agree--you can get that much. If you call it 10-15 fps, I'd say you weren't comparing equal strings.
To answer the original question, each do have substantial up's and down's. Flemish is more adjustable--nice, especially when tuning a new bow. Flemish is generally quieter (properly made), especially on a recurve.
Endless are easier for most folks to make precisely with less practice. Flemish seems to take a little more practice to get right. Endless settle in quicker and don't retract (in the HMPE materials at least) when you un-string your bow like flemish strings will.
Both get the job done. It's mainly a matter of personal preferance. I shoot flemish most of the time, but tinker with endless. I have one bow that just doesn't look right with anything but an endless string on it.
That's one of several reasons it's nice to know how to make your own strings--endless and flemish. You can tinker with both and see which you like best.
Chad