Because under the old, existing rules, each Estate got one vote in the overall decisions of the Estates General. The 1st Estate (clergy) would get 1 vote, the 2nd Estate (nobility) would get 1 vote, and the 3rd Estate (all others, commoners), would get 1 vote. The clergy and nobility routinely colluded with one another to maintain their hold on power. The members of the 3rd Estate, though they were 98% of the population, thus would get outvoted.
The 3rd Estate delegates at the Estates General in 1789 demanded that voting be by head count of all delegates, rather than just one collective vote per house. That way the 3rd Estate would have enough delegate votes to sway decisions.