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Mainly because of 3 reasons
1. R12 has more code than 11i, so this will account for an increase in the SYSTEM tablespace.
2. R12 has additional modules over 11i, so this will account for increases in DATA and INDEX (and other) tablespaces for the new tables and indexes.
3. Data in existing modules (such as Financials) has been rearchitected and additional tables/indexes have been created and the upgrade populates them, while leaving data in the old unused tables. This will also account for an increase in size of the DATA and INDEX (and other) tablespaces.