The best replacement for hypothalamus is thalamus.

The best alternatives to hypothalamus are rated as following:
★★★★★  thalamus
★★★★  pituitary gland
★★★  pituitary
★★  hippocampus
★  ventromedial hypothalamus
★  medulla
★  posterior hypothalamus
★  central nervous system but not the anterior pituitary
  pituitary the master gland
  lateral hypothalamus

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Speaking about hypothalamus, one probably shouldn't forget about pituitary gland.

Other search terms related to hypothalamus and their ratings are:
★★★★★ pituitary gland
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hypothalamus
thalamus
pituitary gland