I'm not sure I see where you're going. Thomas' reading of Brown v. Board of Ed seems identical to mine:
Public school systems that separated blacks and provided them with superior educational resources--making blacks "feel" superior to whites sent to lesser schools--would violate the Fourteenth Amendment, whether or not the white students felt stigmatized [...]
[...]
Regardless of the relative quality of the schools, segregation violated the Constitution because the State classified students based on their race.
But further: the circumstances of these cases are wildly different. Brown v. Board of Ed was about active, de jure segregation of black people and white people. Missouri v. Jenkins was about a school district that became majority-black as a result of white flight.
Kennedy's concurrence was illuminating: it seems to allege that the plaintiff and defendant in this case (the students and the KCMO school district) were colluding: an accident of venue was the only reason KCMO's school district was named defendant, and the actual, unnammed, shadow defendant was the state of Missouri, which was being coerced into funding an otherwise wildly unfundable mandate to create extravagant inner city schools by judicial fiat.
Thomas, Kennedy, and Rehnquist all put heavy attention on the circumstances of this case, that the federal judiciary (a) probably can't impose state taxes by fiat as a backdoor to legislation, and (b) clearly can't do so under the auspices that demographic "segregation" was equivalent to legal segregation. That all makes sense to me.
The FBI, air traffic control, copyright extensions: these are all well supported by legislation. They were not imposed as a backdoor by fiat by an activist court.
In particular, I dispute the "disparate impact" theory underlying the court's reasoning, namely that segregation does not qualify as equal protection because it is is disproportionately harmful to blacks.
I don't think disproportionate harm is required or relevant. My first principle is that equal protection is violated when gov_decision(circumstances, race1) != gov_decision(circumstances, race2).
Because of this, it would be relevant for me to cite Clarence Thomas in Missouri v Jenkins: http://supreme.justia.com/cases/federal/us/515/70/case.html But since Brown v. Board doesn't take this same first principle, citing them wouldn't help you understand my views (even if I agree with the outcome).
Presumably, if I knew your first principles (and if we are both completely rational, and you are intellectually consistent), I could predict your opinion on any given case. And that's the question Nirvana was asking - what are your first principles?