Obviously, you could increase the max_execution_time in php.ini.
You can improve performance by cron-based archiving (i.e., disable the browser triggered archiving).
You could also increase the max number of mysql connections, and create a bootstrap.php file in your Piwik folder containing:
<?php
// PIWIK_ENABLE_SESSION_START
// - Allows dashboard to parallel load widgets increasing responsiveness
// - Note: requires more concurrent mysql connections (see my.cnf's max_connections)
// - default is enabled; set to 0 to disable
define('PIWIK_ENABLE_SESSION_START', 0);