Lately in my games I barely notice the setback from Scientific Method.. Really if you prepare yourself, or react accordingly, it's not such a setback after all.
I don't believe it should give you a bonus.. In fact, if it represents a new kind of thinking and way of doing scientific research, that kind of thing usually comes at a cost, as you adapt to the new ways, fight people clinging to the old ways (figuratively fighting), etc, you're bound to encounter obstacles.
It all makes sense to me. Those obstacles? You fight them with free religion, moving from a specialist/farming economy to a cottage/corporation/trade economy backed by your emancipated workers who grow your cottages to town super fast, and the same workers being happy and productive in those towns thanks to Universal Sufferage (+1

) and Printing Press (+1 or is it +2?

"), not to mention the +100%

from freedom of speech (doesn't that give extra

too? I can't remember...)
That's the synergy SM is part of, and why it isn't really that much of a setback in the grand scheme of things.
Narmox