They demolished the crossing of I90 just south of the trestle in Bellevue. And now it looks like they're putting in a pedestrian bridge to replace it. I'm not sure why they had to remove the tunnel in the first place. I used to cross it and hang out over the southbound lanes with friends.
The Kirkland section of the trail actually gets a fair amount of use as a bike and walking route and connects sections of Kirkland that weren't easy to connect before. With the South Kirkland park and ride to at the south border I know a few people who used it to bike to the bus system.
Kemper Freeman I think has a lot to do with why the train line wasn't used for light rail.