I think crowded is a relative term. It's only Niseko that really is regularly crowded. Everywhere else in Hokkaido, is very quiet. Sure, occasionally on holiday weekends there are lines for the lifts at a few places, but that's due to old lift infrastructure and not volume of skiers. You'll always get freshies.
The population density of Hokkaido is tiny compared to the rest of Japan, so outside of the tourist visitors to Niseko area, there are very few skiers at other hills. The resorts in Honshu are close to some of the largest and most densely populated urban areas on earth, so they get alot more crowded.