I've just finished up the Bertil Roos 3 day school and Skip barber 2 day advanced school. Since I didn't do the same program at both schools, I can't provide a perfect comparison, but here are a few:

Bertil Roos provides a lot of open lapping in their intro program. They don't use lead follow sessions or rev limits to get you up to speed. If you already have an idea of how to drive a race car, or you have previous racing experience already, I think this method can be beneficial.

Bertil Roos does not do passing exercises in their 3 day school. Because of this, you need to do the whole 5 day program to get an SCCA Regional License, while with Skip Barber you can apply for the SCCA License after the 3 day school.

Roos has no damage liability in their 3 day program, and a lower damage liability compared to Skip Barber for the advanced 2 day.

Roos cars have digital display instead of a analog tach. The display includes shift lights which help for learning the shift points. It also displays speed, although you shouldn't really be looking at that anyway!

The Skip Barber F2000 used for all advanced programs use a 5 speed sequential transmission, while the Bertil Roos F2000 uses a 4 speed crashbox. The sequential transmission is significantly easier to shift.

The Skippy intro schools use the "Formula Skip Barber" which is basically the same as the F2000 but with a 4 speed crashbox and without wings. I don't think having wings or not in an intro school makes a big difference, especially on a course without a lot of high speed corners like VIR south. Unless you have a lot of experience, you probably won't be getting everything out of the car at the end of 3 days anyway.

Bertil Roos cars have a large windscreen so head buffeting and bugs on your visor are not an issue, like the Skip Barber and most other formula cars.

I felt the Skip Barber cars handled a lot more neutral while the Roos cars understeered.

I thought my instructors at both schools were solid and helpful. I would say my instructors at Skip Barber were more experienced at higher levels of competition.

The roos programs are a little cheaper then skippy.

Both programs were pretty flexible in terms of modifying the schedule as necessary. I had read with skip barber some felt held back by the slower students, but I don't think that's the case, at least not in the advanced school

Otherwise, there was a lot similar between the two schools. I would highly recommend both schools, and I don't feel there are any significant downsides to trying both programs.