In any event, as a civil procedure geek, my immediate reaction is "Wait a minutethis is a first-year-law-school question. The party who files a challenge to an action has the burden of proof. Next case!" Not so fast, though; because the substance of who is challenging whom is often different from the procedural posture of who is challenging whom. Sometimes the actual challenger is the school system, and it just looks like the parents (on behalf of the student) are the challengers because they had to make the first court filing.
What this really comes down to is tension between "outcome-determinative" procedures and civil rights. Individuals with disabilities are a protected class under more pieces of legislation, both federal and otherwise, than I can count conveniently. Setting a hard-and-fast, quasicivilproceduresque rule that the person who first goes to court has the burden of proof is inconsistent with the purpose of the act, and usually unfair to the student; ordinarily, the school system can afford to wait things out, both financially and in terms of what passage of time does to a child's development. Since the underlying act puts the administrative burden upon the school system to demonstrate the adequacy of its efforts, why should entry to the court system change those rules?
I don't pretend this is an easy question. There's a lot to be said procedurally for a uniform rule on burdens of proof; "artful pleading" doesn't just mean making a case nonremoveable! There's also a lot to be said for not letting form and procedure overwhelm substance, because in reality the burden is on the school to demonstrate that it made all efforts (not just those that the local school board felt like making).
Then again, if we didn't make the school systems beg for every dime and then diss the teachers; if we committed ourselves to more and better schools instead of more and better sporting arenas; if we had the patience to wait the ten to twenty years to see if a "new" system or improvement actually had any measurable effect upon the "product" of the educational system, instead of tweaking things every four years to make nice for elections; if fundamentalists of all stripes would stop trying to tell me what my children must believe; if, in short, we actually made education the priority it deserves to be, this would all be a moot point.