I shouldn't have said, "at the end." I should have said, "afterwards." By that I mean while I am stretching and the following day. They do not make a 16 mile run feel like a 12 mile run. Perhaps they make it easier to hit slightly faster paces toward the end of long runs, but you can think of this as practice for what you want to do in a race.
I would argue that you still get all of the aerobic benefit of the extended time running during a long run.
I would also argue that you get all (or nearly all) of the muscular benefit where you need your legs to push you faster and you need your legs to push you late in a long run after you are more fatigued.
I like to think that the reason my legs feel better the following day is mainly because the pounding and impact forces are somewhat alleviated by the shoe. Maybe this would be the same for highly cushioned shoes, but I've never been a fan of those.
If I did a harder long run in the Endorphin Speeds, I still need a rest or recovery day and I can feel that my muscles will not let me go when I try to run (I'm hoping you know what I mean here). The shoe doesn't take that away or alleviate it. But when I'm just walking around and doing other stuff, I don't have soreness like I am more used to when I wear other shoes for a long run (Kinvara, Zante Pursuit, Brooks Launch)