Due to work and life (two toddlers consume a lot of time), I haven't been very active with GalCivIII for the past several months. I came back about a month ago and have quietly absorbed the changes to the game brought on by Intrigue. The changes are fairly significant and offer some excellent changes to game play. Great work, dev team!
I do have a few comments (more likely to come). First, the major change to tourism and the way the economy looks on the summary is kind of confusing.

The confusing part, to me, is that the GDP, Trade Route Income, and Tourism lines are being modified by Taxes--but they are all listed as weekly income.
I'd suggest either separating Taxes from the other items in Weekly Income and indicate that the income is being modified by the tax rate (i.e., 4,797 + 234 + 29939 = 34,970 x 0.07 = 2,447.9). Or just list the already modified amount (i.e., instead of GDP 4,797, list it as GDP 336 (4797 x 0.07)).
Or maybe someone has a better solution. This isn't a big deal, but it took me a while to understand why my Net Weekly Income was so low considering my GDP and Tourism.
The other issue I saw isn't related to Intrigue--I think it's been in the game a while, and it may be working as designed. The "GiveCreditsArtifact" anomaly awards the higher value of 400 credits or 8% of a players credits. With a large treasury, this is crazy overpowered:

I had trouble figuring out where my excessive income was coming from--but this particular turn, I got 5 or 6 "Ancient Riches" anomalies, which resulted in something like a 300,000 credit income. I'm probably going to mod this anomaly, but I thought I'd mention it if anyone on the dev team is interested in tweaking this.
The other issues I have with the game are persistent ones: some goofy inconsistencies remain in the Mercenaries list, and I think the Ideology list could use some TLC.
TLDR: Intrigue improved this game vastly; some minor issues (confusing economy summary; OP artifact) and opportunities for improvement (Mercs and Ideology).