Trott finished six points behind defending champion, the USA's Sarah Hammer, in the six event discipline while Australia's Annette Edmondson completed the podium - an exact repeat of the top three from 12 months ago.
Team-mate Becky James took bronze in the women's keirin to mean Great Britain finished the championships with two golds, one silver and two bronzes, placing them fourth on the medal table.
"I am actually happy with how this has turned out," Trott told britishcycling.org.uk
"I always think - although I do always want to win every single race that I enter - this time before London where was I?
"I was still a junior. And the next year was Apeldoorn and I finished 16th. And then went on to win the following year.
"Although I would've absolutely love to have won, I'm really pleased with how I got on and how I am improving in each event."
James, a double world champion last year, insisted she was happy with finishing third in the defence of her keirin title, another bronze to go with her performance alongside Jess Varnish in the team sprint.
Germany's in-form Kristina Vogel claimed her third win of the week while James was just pipped on the line by Australia's Anna Meares.
"I'm really happy," she said.
"It's always disappointing not to win but Kristina Vogel has been flying all season. She deserved it."
- Sports & Recreation
- Becky James
- Annette Edmondson