I wonder if the best approach is not to use all great spies for scotland yards. That's 100% EP boost, a level you can't reach for beakers until superconductors.
And that's why I would use the Great Spies to build Scotland Yards across the board.
Using only the Great Wall as GPP generation for the first one, you're probably not going to be in a position that would (heavily) benefit from the Scotland Yard, so I think the issue isn't about using the GSpy for SYs in general, but what to do with the first one.
Assuming you're not using the overpowered Infiltrate feature, all I can say is to use that Great Spy to explore. It seems counterproductive, but those Great Spy pops will be rare until Constitution and Democracy, and I feel the EE starts breaking down with Democracy.
Exploration is the only option I would consider outside of building an SY. Settling just doesn't seem nearly as effective. Especially when considering AI reactions to EP buildup.
Slow, long-term EP buildup against a specific AI is usually matched by that AI, to some extent, leaving you with a higher base EP value to reach before you start hitting the cost reduction modifiers.
A commerce approach avoids this, using very low passive EP generation to keep those base levels low, and by employing the slider to generate a massive burst of EP, for an overall lower EP expenditure for the same return.
A commerce approach also seems to have a stronger ability to self-research as appropriate.
Gliese, Liz sounds good. I definitely believe FIN to be the premier EE trait, though FIN has very strong applications in other approaches. One advantage of the EE is that because it requires less commerce to achieve the same tech score, it does not need a strong trait such as FIN to support it. But FIN would have a much stronger ability to mix espionage with self-research, and seems less dependent on the AI to progress.
What other trait goes well with it, however? I'm thinking SPI is better than PHI. I'm thinking of religion swaps here. -15% for a city having your state religion when your target has a different state religion. -25% for a city having your state religion and you have the holy city of that religion, regardless of whether it's your target's state religion or not.
ORG might work well for the cheap courthouses. I can see where IND might be desirable on higher levels to ensure building the Great Wall, though obsolete would be better able to answer how necessary IND is in that.