Laborious You were not as I thought you would be. This is the most idiomatic version. Laborious You were not as I had thought you would be.
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LaboriousYou were not as I thought you would be.This is the most idiomatic version.
LaboriousYou were not as I had thought you would be.This is also correct, but less common in my judgment.
LaboriousYou were not as I thought you were.This is least idiomatic of the three, but it's gramma
LaboriousdifferencePast and present. Nothing more mysterious about them.