I just commented about this. We have one of these, and it's new, but the layers and layers of recent roadwork make it extremely confusing. I've seen people driving in the wrong lanes around the intersection. Thankfully there are plenty of businesses nearby (it's not a highway) so I'm sure those errors are corrected quickly, but it's dangerous.

That said, the intersection on average seems to be more efficient than it was before.

How hard would it be to just build a pedestrian tunnel underneath it and avoid the problem altogether?

There's an interstate underneath, which is the reason there's a complicated intersection at all. Building another bridge level might be safer for pedestrians, but also more expensive in construction and maintenance, plus now you need to worry about clearance. Perhaps building a footbridge over the interstate a bit down the road could help, but then it adds a detour...there's a tradeoff in each of the cases.

In case this isn't sarcasm:

1. Based on the article, and the parent comment here, it's not about the pedestrians (in this case).

2. Even if it were, it'd be much more difficult. Tunnels and bridges must be 10x - 100x more red tape and cost than surface-only structures.

I think you would want to go over, not under. It seems easier to build a 30' bridge that can support foot traffic than to dig a 30' tunnel that needs to support semis driving over it.

One thought, if there isn't a high volume of foot traffic, is to just the fact that these are typically paired (one to swap lanes, another to get them back to the "right" side). Put a pedestrian crossing in the middle, and you can stop traffic from both directions at once. Bonus points that cars are supposed to stop pretty far away, so pedestrians could see someone running the light from much farther away rather than having to wait til they're 15 feet away to tell they aren't going to stop.