The Uchiha are stronger overall but people using the example of Madara, Itachi and Sasuke are stupid, they are once in a generation geniuses, they don't represent the clan as a whole. In part one however, it was said by Kakashi that the Uchiha were the strongest in the village and the clan's reputation suggests they are stronger.
Like the Uchiha clan, the Hyuuga mastery of the byakugan would be a different stages, Neji was also a genius, all of the branch house wouldn't be able to see rotation or see as far as far as others, most of them certainly wouldn't be able to use 8 trigrams 64 palms, judging by Hiashi's reaction to Neji using it.
The Uchiha clans mastery of fire techniques and genjustu prowess is something most of the clan would have while techniques like rotation aren't, so as a clan the Uchiha are definitely stronger.