One of the purposes results of the sankin-kōtai was to sap the financial resources of the daimyōs and make them too poor to rebel. The cost of living in Edo was high, and the frequent travel in large groups as well as need to maintain and staff two lavish residents (one in the domain, one in Edo, many had a third in Ōsaka but I don't believe it's mandatory) was a huge financial burden on almost all the clans. It worked so well that it contributed greatly to clans and samurai debt, and a couple of times during crisis the terms were relaxed or placed put on pause.

As part of a series of reforms in 1862 to respond to both internal and external pressures, the terms of the sankin-kōtai was relaxed to only 100 days every 3 years for daimyōs and their families were allowed to return to their domains. The idea was to give the bakufu and clans the financial resources to conduct reforms, especially military reforms.

This contributed to the fall of the bakufu, as allowing the clans to take back their hostages both showed the weakness of the bakufu and of course remove the worry of the hostages being executed if orders weren't followed. Finally the mass exodus of people from Edo contributed to the sharply raising prices along the roads to and from Edo. The rising prices led to civil unrest at critical moments in the bakumatsu.

EDITED: See below.