This should be obvious, but intelligence isn't closely correlated with brain size within the same species.
Also the correlation that does exist is in the ratio of brain size to body weight. Small people can have smaller brains without being less intelligent.
The configuration of the brain also matters.
I've read that breeders of dogs and other animals know that you can selectively reduce an animals size but, their brains don't reduce proportionally. That's why it's very unlikely that the hobbits are dwarf branch off humans. They're probably a branch off the much older Erectus. If so, the dates would indicate they outlived Neanderthal by at least 10,000 years.