“Like the Federal Rules of Criminal Procedure, the Federal Rules of Civil Procedure are as binding as any statute duly enacted by Congress, and federal courts have no more discretion to disregard the Rules' mandate than they do to disregard constitutional or statutory provisions." Chambers v. Nasco, Inc., 501 U.S. 32, 66 (1991).
The civil and criminal rules of procedure are established by the U.S. Supreme Court, which promulgates them under authority delegated by Congress in 28 U.S.C. 2072. Some rules provide the courts more flexibility in their application than others, but the courts may not simply ignore them any more than they could ignore a Supreme Court precedent.
For instance, in a case where the trial court dismissed criminal charges based on prosecutorial misconduct, the government appealed, arguing that the misconduct hadn't prejudiced the defendant, and Criminal Rule 52's "harmless error" rule requires the court to essentially ignore errors that don't effect the defendant's "substantial rights." The defendant argued that the court's supervisory authority permitted it to dismiss the case to deter future misconduct.
The Supreme Court reversed the dismissal, agreeing with the prosecution that a court has no authority to dismiss the case based on error that the rules of procedure order it to ignore: Rule 52 is, in every pertinent respect, as binding as any federal statute. "Courts have no more discretion to disregard the Rule's mandate through the exercise of supervisory power than they do to disregard constitutional or statutory provisions through the exercise of such power." Bank of Nova Scotia v. United States, 487 U.S. 250, 250 (1988).
Other courts have concluded that this standard applies to the Federal Rules of Civil Procedure, as well. See, e.g., Stone Container Corp. v. United States, 229 F.3d 1345, 1354 (Fed. Cir. 2000) ("[T]he Federal Rules of Civil Procedure, like the Federal Rules of Criminal procedure, are “as binding as any federal statute.”); S.E.C. v. Selden, 484 F. Supp. 2d 105, 107 (D.D.C. 2007); Sieb's Hatcheries, Inc. v. Lindley, 13 F.R.D. 113, 119 (W.D. Ark. 1952); Westland Oil Co. v. Firestone Tire & Rubber Co., 3 F.R.D. 55, 56 (D.N.D. 1943).
tl;dr: The Rules are rules of procedure. They must be adhered to.