I have been doing a bit of profiling on a site I am working on which extensively uses views.
Views takes up about 2/3 of the processing time even with the views caching on. Are there best practice ways to speed up views, or things which are known to cause performance hits.
I should add that the views are solr views, so this is a question mostly about the views architecture rather than optimizing queries.
Have tried using APC, but it didn't change the execution time much.
Using advance caching techniques will not only improve query intensive views but will improve overall performance of the website.
But the above can be a separate issue.
First try to indentify the problem as stated by @Daniel Wehner. Then again also look at the issue queue of the view3 to see it has any conflicting module, that is slowing down the query.
Also disabling some modules and trying to see the performance difference can help you identify the culprit. It has happened with me. A facebook module was making my views very slow and the page rendering time was awfully high.
You first should find out where the performance bottleneck is.
See http://drupalperformanceblog.com/drupal-xhprof-profiling about the article.
Once you have the problem it's possible to fix it. You wrote that you had enabled views caching: Which kind of caching output or query cache?