Anovulatory Cycles: This is a common condition in adolescents, especially within the first few years after menarche. The presence of physiologic cysts on ultrasound and the absence of hyperandrogenic signs support this diagnosis. The patient's age, recent menarche, and hormonal levels (FSH and LH) also align with anovulatory cycles, which are often seen in the early years following menarche as the hypothalamic-pituitary-ovarian axis matures.

Hypothalamic Amenorrhea: Although the patient is having frequent menses, the intense exercise regimen and skipped meals could potentially disrupt the hypothalamic-pituitary-gonadal axis, leading to irregular menstrual cycles. However, the presence of menses, albeit frequent, and normal prolactin levels make this less likely than anovulatory cycles.
Polycystic Ovary Syndrome (PCOS): While PCOS is a consideration in adolescents with irregular menstrual cycles, the absence of hyperandrogenic signs and the normal ultrasound findings (showing only a physiologic cyst) make this diagnosis less likely at this time. PCOS diagnosis in adolescents requires a careful evaluation over time due to the variability in menstrual cycles and the potential for late manifestation of hyperandrogenism.

Pituitary or Hypothalamic Tumors: Although rare, these conditions can cause significant morbidity if not diagnosed. The normal prolactin level reduces the likelihood of a prolactinoma, but other tumors could still be present. The absence of other symptoms (e.g., headaches, visual disturbances) makes this less likely, but it remains a critical diagnosis not to miss.
Thyroid Dysfunction: Thyroid disorders can affect menstrual regularity. Although not directly indicated by the information provided, thyroid function tests are often part of the initial evaluation for menstrual irregularities to rule out hypothyroidism or hyperthyroidism.

Premature Ovarian Failure (POF): This condition is characterized by the cessation of menstrual cycles before the age of 40. Given the patient's age and the presence of menstrual cycles, this diagnosis is highly unlikely but could be considered if there were elevated FSH levels indicative of ovarian failure, which is not the case here.
Androgen Insensitivity Syndrome or Other Disorders of Sex Development: These conditions are rare and typically present with primary amenorrhea or significant virilization, neither of which is described in this patient. However, they remain in the differential for any adolescent with irregular menstrual cycles until ruled out by clinical evaluation and appropriate testing.