Microsoft Store for SharePoint. We intend to be flexible on pricing for IntelliGantt users so for the store we do a simple $1.99 per user per month. This should make it very affordable for small teams and provide a consistent revenue stream for support and new features. Microsoft has done a nice job integrating it into your SharePoint experience for Office 365 and its quite easy to install IntelliGantt for SharePoint and try it out. However, things are not set in stone as we're just starting off with the Microsoft Store for SharePoint.
The other option for you is to simply load our IntelliGanttSPAddIn.app file to your SharePoint server, be it in house or Office 365. Same tool and functionality, just a different way to acquire, license and deploy.
Finally, we have had customers who use site collections to organize smaller efforts of works, which means rather than 1 site collection with 365 sites, they have 5 site collections with 73 sites each. What we are thinking for that case is to introduce an 'instance' license. That is, up to 365 instances of IntelliGantt placed on a page in sites across site collections. Something like $365 per year again for 365 instances of IntelliGantt seems to make sense.
The last thing we want to do is make it difficult to figure out which license to purchase, but SharePoint is used in such a variety of ways that a 'one license fits all' strategy is too constricting as well. Let us know what you think!