Zoe and sassafrass—science and magic mixed together and very sweet.

Also consider Brambly Hedge. Again a book that somewhat defies categorization between picture book and chapter book, but absolutely perfect for kindergarten.

First of all, don't overlook some of the older, longer "beginning readers." They may be short, but there's decently complex text/plot in Frog and Toad and other works by Arnold Loebel. Same with Mr. Putter and Tabby, Henry and Mudge, and Annie and Snowball. All those have multiple little episodes per story, so are kind of like chapter books. Same with the charming and delightful Thimbleberry Stories by Cynthia Rylant which straddles the boundary between a picture book and a chapter book.

Want to second the recs from 20:16, 20:57, and 21:34. All so good! Flat Stanley and McBroom would be the shortest of those, if length is an issue.

Also seconding or thirding:

Princess in Black
Clementine
Ramona
Mercy Watson

Adding in:

Anna Hibiscus
Ways to Make Sunshine
Heartwood Hotel
Tuesdays at the Castle
The Ordinary Princess (not a series)
James Herriot's Treasury for Children

The Owl Diaries
A second vote for Mercy Watson
More stories than chapters but Frog and Toad

Dragon Masters series