Suphp + suexec is a dupliacet effort. If you want to use suphp, then suexec is not needed.
If you use cgi-php or fcgi-php, then you have to activate suexec.
Starting with ISPConfig 3.0.3 Beta you will have a inpit field for custom php.ini settings in ispconfig which works also for php-cgi and php-fcgi.
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