After "I wish" follows past tense to express an irreal wish, ie a wish that can't come true. In written language: I wish father were** here. In colloquial language this were** is replaced by was*: I wish father was* here.

were** = genuine Past subjunctive Was* = Past indicative as substitute for subjunctive.

After I thought + clause we have something similar.

• We thought you were the type for the job. A Past indicative in the clause makes no sense.Only as a Past with subjunctive function the sentence makes sense.

A lot of good examples would be necessary to show this in a convincing manner.

After "I wish" follows past tense to express an irreal wish, ie a wish that can't come true. In written language: I wish father were** here. In colloquial language this were** is replaced by was*: I wish father was* here.

were** = genuine Past subjunctive Was* = Past indicative as substitute for subjunctive.

After I thought + clause we have something similar.

• We thought you were the type for the job. A Past indicative in the clause makes no sense.Only as a Past with subjunctive function the sentence makes sense.

A lot of good examples would be necessary to show this in a convincing manner.

Here's a link to BNC with 50 examples for "I thought I was ...". I think there are examples among these that show that "I was" can't be understood as a normal Past indicative.

BNC