I'm not 100% positive on this, but I think there is a misunderstanding as to how speed burst factors into fatigue in the game.
Holding speed burst doesn't necessarily wear anyone out because all it can do is get you to top speed, which can actually be done without holding it. You're going to exert more energy on each run, but once at top speed it makes no difference if you hold speed burst or not.
Fatigue has more to do with player use and amount of distance covered. If you have 15 carries of 20 yards then you're going to be pretty gassed whether you used speed burst or not. The same goes for teams that pass a lot and run more plays on offense -- your receivers are going to get tired more often.
Keep in mind though, if you're getting a lot of long runs -- you don't have to run the ball for as many carries. And if you're racking up that many yards, fatigue is likely not a big concern for you.
Personally, I wouldn't worry too much about fatigue when you use speed burst. If you need to get to top speed, then use it.