I recently had a client who had been told by someone that the innovation patent was a useful tool for protecting patents. There's no doubt that the system can be attractive. See my post of 10 June 2010 and others. Perhaps the most significant reason for that is that the innovation patent can be ready to enforce in as little as two to three months from the date of filing the application.
However, there lurks an often overlooked danger. The innovation patent is granted and published in very little time. In some cases, grant and publication occurs in as little as a month. This may not be an issue where an invention can easily be discerned in its commercial application. However, software is often best kept under wraps for as long as possible, allowing the product to develop recognition and traction in the market place. A requirement of our Patents Act is that the patent specification must disclose the best manner of performing the invention known to the applicant at the time of filing the application. So it's not possible to get away with keeping key aspects of the invention secret if you want to file a patent application.
Standard patent applications are only published 18 months after the earliest date on which a patent application covering the invention is filed. In the world of software, this can be a long time, allowing commercial objectives to be achieved while detail of the invention remains confidential. However, if you've decided to go the innovation patent route, that confidential information will no longer be so in an little as a month after the application has been filed.
So, budget permitting, my recommendation is that you file a provisional patent application, get the software commercialised as soon as possible and file a standard patent application based on the provisional patent application. If you need to enforce your rights, you can easily file a divisional application for an innovation patent based on the standard application (see my post of 21 November 2007).