1. Microsoft Project is only for bigger organizations because it’s incredibly expensive.
How about MAPS subscription which gives you, among tons of other licenses, a license for MS Project Server and 10 sits of MS Project? This actually scales up to 10 people preparing MS Project Schedules and unlimited number of people who just update tasks (via Web Access). And that all for stunning price of $300. When you outgrow the initial setup you have to buy additional licenses for a standard price but it will take some time.
2. Microsoft Project has no real collaboration features.
MS Project as a desktop application has no collaboration features – that’s true. But if you take some time to setup MS Project Server you instantly get all the basic collaboration features (and I guess many advanced ones too). Of course it isn’t deployed in the cloud which is quite a disadvantage these days but still the argument doesn’t seem valid for me.
By the way this is one of areas where Microsoft completely screwed. In the early 00s they had everything to bring so called Project Management 2.0 to the table but missed the chance.