Christian, I would prefer to say great opportunities ahead for Mathematica!

If you look at a site such as arXiv.org I don't think you'll see any CDF files available. In the future I believe you'll see a lot of them and eventually they will replace PDF as the dominant form of technical document. Why? Because, as you probably well know, with their active and interactive capabilities they are far superior to other documents. But it will take time and at first you may have to do an end around, such as make them available from your own web site. People have to see them but once they see them, what's not to like about them? Of course it will help if the initial examples are well written, perhaps mirroring a paper in interactive form.

Any serious paper is likely to have associated customized calculation and display routines. It is possible to transmit applications with packages to readers and they can install these in the Wolfram Research/Wolfram CDF Player/10.0/AddOns/Applications folder. Then the CDF document can use your packages. I'm not certain, however if this is approved by WRI. You can't just unzip into that location. You have to copy the folder and give Administrator permission. It would be helpful if the free player created a $UserBaseDirectory where readers could place any additional packages outside of the Wolfram files.

Another problem is, if you have Mathematica installed, to get the player to open a CDF file in the free player, without access to Mathematica applications and packages, to test what the experience would be for a reader without Mathematica.

I suspect there are a number of tune-ups needed to make this a smooth experience for everybody.

Mathematica Cloud is another approach but I just don't know enough about it yet. WRI really doesn't give enough specific information, especially as regards developer packages.