EAU CLAIRE, WIS. — If ever a big, fun summer music festival called for Jeff Tweedy to cheer on the dreary, thundery skies, Eaux Claires would be it. The Wilco frontman even sounded excited as he introduced his band’s morbid and downtempo fan favorite “Via Chicago” on Saturday night in weather that came across with equal misery.

“Usually we play it under beautiful blue skies, and it really bums people out,” he said. “This is [expletive] perfect!”

Hosted once again by Justin Vernon of Bon Iver fame — Eau Claire’s own gray-sky indie-rock star — the second day of the third annual Eaux Claires Music & Art Festival featured a drizzly tone throughout much of the day. Wilco’s trove of dour songs topped off a lineup that also found Paul Simon reinventing many of his saddest favorites into lilting classical music pieces, and Feist skipping most of her upbeat hits to instead perform her raw and sometimes intense new album in its entirety.

Despite the stormy weather and the inordinate amount of gloomy music, though, Eaux Claires once again proved to be a clever and fun alternative to the glut of predictable music festivals around the country.

Pleasant surprises on Saturday included an unannounced appearance by beloved twang-rocker Jenny Lewis on a small stage set in a forest, backed by a Minnesota all-star band including JT Bates and Mike Lewis. Deeper in the forest, some of the 15,000 or so attendees wandered along hiking paths where art installations were hidden amid the foliage, and where the harmonious three-woman vocal folk group Mountain Man performed a cappella on a small stage that could have been mistaken for a firewood storage shed.

Unfortunately, the weather for the festival truly was unpleasant. A fast and fierce rainstorm marred an all-star tribute to John Prine on the opening night of the festival Friday. The clouds returned with a vengeance Saturday afternoon as Detroit’s quirky spazz-rapper Danny Brown performed on one of the two main stages. Brown played on at a determined gait amid the downpour, which only made his set seem more madcap.

That sudden late-afternoon squall and a foreboding forecast forced the cancellation of many of the side-stage events. Too bad, but did anyone really want to skip a rare one-off performance by a two-time Rock and Roll Hall of Famer to instead see our ubiquitous host Vernon show off his beatmaking skills with Twin Cities hip-hop producer Psymun?

That unique appearance by the elder Simon — delayed as crews swept water off the stage — paired the legendary singer/songwriter with yMusic, an innovative classical sextet also from New York that has recorded with the likes of Ben Folds and Sufjan Stevens. The ensemble rearranged a dozen of Simon’s mostly older tunes with strings and wind instruments, turning the set opener “America” into a dramatic epic worthy of a John Ford western and giving “Mrs. Robinson” a darker, bluesier makeover that actually better suits the lyrics.

It was a genuine thrill to hear Simon in such a unique configuration, but anyone looking for the buoyant, bubbly grooves and melodies of “Graceland” came to the wrong festival. By the time he got around to singing, “Hello darkness, my old friend,” at the start of “The Sound of Silence,” it even sounded redundant (but great, too).

With Simon standing beside the stage watching her through most of her set, Feist brazenly barreled through her stripped-down, tensed-up new album “Pleasure” for her first Upper Midwest appearance in five years. The full-album performance was the only one on her tour so far, and she said she intended as a special treat for “the festival I’ve been hearing about for two years.”

As Feist’s songs rolled on, they picked up in tempo and volume, with the playfully Dylanesque “Baby Be Simple” giving way to the adrenalized closer “Young Up,” which she described as the record’s “chase scene.” She finished with two of her prior album’s jagged highlights, “My Moon My Man” and “I Feel It All,” capping off one of the most memorable and meaningful sets in Eaux Claires’ three years.

There were some throwaway moments Saturday, too. The midafternoon performance by Seattle’s Bon Iver-like art-pop balladeer, Perfume Genius (Mike Hadreas), came off like an overwrought mess with overthought, showy song arrangements. A small portion of the crowd reacted rapturously while the rest just looked confused.

The audience mostly looked bored sprawled out on the grass listening to the mild-mannered rambling of Berlin’s classically tinged ensemble Stargaze. Things certainly heated up, though, when ex-Minneapolitan rapper Astronautalis joined the Berliners in a terse, freestyled homage to the prior day’s not-guilty verdict in the Philando Castile shooting.

Without an actual Bon Iver performance this year — Vernon instead lined up a July 22 set at Rock the Garden in Minneapolis — the marquee slots at Eaux Claires 2017 were left to Chance the Rapper on Friday and then Wilco for the Saturday finale. The Chicago vets literally did benefit from the bad weather, too: The altered schedules wound up giving them about an extra half-hour to play.

Tweedy & Co. used the time to great effect, delivering slow-building showpieces such as “Spiders (Kidsmoke)” and “The Art of Almost,” each seemingly synchronized to far-off lightning flashes that repeatedly lit up the dark clouds. Let the other festivals get the sky-blue-sky performances out of Wilco; this one was indeed perfect for Eaux Claires.