Has Puerto Rico experienced fewer privileges and autonomy than other US territories?
It's a very broad question. The way the question is worded the answer would yes.
The United States invaded Puerto Rico in July 1898 with little opposition (seven American soldiers died ). By Oct 1898 the United States signed an armistice with Spain granting it the possession of the Island.
- 1917 the US Granted full US citizenship to the citizens of Puerto Rico.
- 1948, Puerto Ricans could elect their own governor
- 1952 the U.S. Congress approved a new Puerto Rican constitution that made the island an autonomous U.S. commonwealth, with it's citizens retaining full U.S. Citizenship.
- 1967 and 1993, popular referendums were held for independence, with the majority of Puerto Ricans supporting the continuation of their special status as a U.S. commonwealth.
Puerto Rico has experienced fewer privileges than some other U.S. Territories. If we compare Puerto Rico with Hawaii both of which became territories around the same time.
From 1898 - Jan 1949, Puerto Rico had an appointed Governor and its people were denied the right to elect their own leadership. Hawaii for example entered the union in 1890 and was permitted to elect Sanford B. Dole, their first governor in that same year. Many territories enjoyed a much faster path to representative governance inside the federated system.
Citizenship was also granted to all citizens of the Republic of Hawaii for example, as of 1898 immediately in 1890 when it became a US territory. It took, 20 years (1917) for Puerto Ricans to gain US citizenship after becoming a territory.