MVC router class performance

$params = (count($url > 0)) ? $url : "";

Is this really what you meant to say? This looks like it should be

 $params = (count($url) > 0) ? $url : '';

The second version treats the $url variable as an array. The previous code treats $url as an integer and then treats a Boolean expression as an array. This is problematic because both count(false) and count(true) return 1. Meaning that the first version is the same as $params = $url.

This was the only functional comment that I had on the code. Everything else is just style. It's possible that if you fleshed out a problem statement describing what the code is supposed to do that someone would have additional functional comments.

            if ($this->validateURL()) {
                $class = (isset($url[1])) ? $url[1] : $this->get('defaultController');
                unset($url[1]);
                $method = (isset($url[2])) ? $url[2] : $this->get('defaultMethod');
                unset($url[2]);
                $params = (count($url > 0)) ? $url : "";
                unset($url);

                if (class_exists($class)) {
                    $controller = $this->app->getInstance($class);
                } else {
                    exit("Class not found");
                }
                if (method_exists($controller, $method)) {
                    if ($params !== "") {
                        call_user_func_array(array($class, $method), $params);
                    } else {
                        $controller->{$method}();
                    }
                } else {
                    exit("Method not found");
                }
            } else {
                exit("URI chars not allowed");
            }

You could reduce your indentation by using early exits instead of if/else.

            if (!$this->validateURL()) {
                exit('URI chars not allowed');
            }

            switch (count($url)) {
                default:
                    $method = (isset($url[2])) ? $url[2] : $this->get('defaultMethod');
                    unset($url[2]);
                    // 3 or more fall through to 2
                case 2:
                    $class = (isset($url[1])) ? $url[1] : $this->get('defaultController');
                    unset($url[1]);
                    // 2 or more fall through to 1
                case 1:
                    $params = $url;
                    break;
                case 0:
                    $params = '';
                    break;
            }
            unset($url);

            if (!class_exists($class)) {
                exit('Class not found');
            }

            $controller = $this->app->getInstance($class);
            if (!method_exists($controller, $method)) {
                exit('Method not found');
            }

            if ('' === $params) {
                $controller->{$method}();
            } else {
                call_user_func_array(array($class, $method), $params);
            }

I also changed the order of the final if/else. I try to avoid the if not else form. An else is implicitly taking the logical not of the test expression. So if the test expression is negative, this means that the else is the negative of a negative. I often find it more readable if I reorder the clauses such that the test expression is positive.

I prefer to use single quotes if I can. There's a slight performance benefit, but the chief advantage is that it is easy to see that no variable interpolation will occur. With double quotes you have to examine the string to tell that.

I don't know that the switch version is better than what you had originally, but I wanted to include it as a possibility. I find it a little clearer, but it is more code. On average, it may give a very slight performance advantage. Probably not enough to matter.