...In the mid 70's? someone defected in Japan with a Mig-25, almost crashing
into a commercial jet at the Tokyo airport.
Viktor Belenko and it was Hakodate Airport in northern Japan. He overshot the runway, damaging the landng gear, but he was almost out of fuerl and couldn't go around (plus, he didn't want to get shot at).
Well of course the USAF pretty much went over it with a fine tooth comb before returning
it. They found out the environmental system sucked,
The pressurized flight suit worked fine, I've never read that it didn't (athough the current F-35 program seems to be having problems). Possibly you are referring to the sophisticated environmental system for electronics that the Mig-25 did not have because its vacuum tube electronics did not need them? The vacuum tube radar was far more powerful than any on any U.S. aircraft, 600 KW continuous, with tremendous ECM burn-through power (the F-4 had a 30 kw radar).
the build quality suffered greatly
Probably you are referring to the fact that the Soviets did not use blind rivets everywhere, as in a US aircraft, but only where they were needed? Or the fact that titanium was only used where its high temperature properties were needed?
and the engines were prone to needing replacement after a few missions.
Not when flown according to guidelines (they did have a shorter life than U.S. engines though, true).
In other words, other than speed, it kind of sucked.
How about extremely high operating altitude, out of the range of most other combat aircraft?
It has a very creditable (though limited) combat record. But 75% of all Mig-25s were recon versions, and there their performance and record is outstanding, remaining in service in India until recently. It remains one of the most successful combat reconnaissance planes of all time.