When talking about setbacks in the Waystone Project, or the lack thereof, I think it comes down to that rarest of possible things in a quest: the players actually making good decisions. (Less rarely, not entirely on purpose.)
Internal political problems from Laurelorn? The thread made a conscious decision to shore up anti-isolationist support not just in bringing elves onto the Project, but bringing other Houses onside by way of trade.
External political problems from Imperial factions? We're based in an isolationist faction they aren't even allowed into. I think it's quite likely that the first time the Cult of Sigmar had even heard of the Waystone Project, was when we were rolling Waystones out across Praag, Sylvania, and Black Water.
Internal political problems within the Project? We actually knocked this one out of the park more or less by accident. We had what seemed to be a mostly-flavour vote on how much money to spend on doing up the Project's building. We decided that Mathilde's never heard of a Vow of Poverty she respected, and dropped 600 gold on the nice curtains. IIRC Boney later revealed that members of the Project who didn't get on could just avoid each other in comfort because we'd essentially outfitted a mansion in luxury.
Political problems with the rollout? We've started by dropping Waystones in a bunch of the most heavily corrupted areas possible, across multiple polities, dodging plausible grumbling about favouritism.
The possible threat of enemy action? This one isn't a decision we made, but an ongoing decision by possible antagonists that long-term infrastructure projects aren't their problem.
Ulthuan not being too upset about us poking the Network is about the only thing that could feasibly have gone poorly. That it was first noticed by Teclis, who likes humans might have helped - or might not have, given Teclis' famous charisma. Eltharion taking an interest was admittedly very much lucky there, but no one involved was going to listen to Ulthuan if they'd tried to say "no", and by that point we were already producing results, making possible Asur bribes less tempting.
Apparently we might expect more politics when we do further rollouts. If we want to do a clean sweep of good decision making defanging opposition, I'd suggest continuing to pick multiple locations to deploy to each turn, so people don't complain they're getting passed over.