If this is really just an umbrella term for a bunch of independent research, that's different. The problem with a big project organization is that the administrative overhead involved in coordinating all of those 90 institutions will eat up valuable time and research dollars. And with no clear roadmap to guide priorities, that overhead won't provide any benefit. There's too much basic research left to be done before people start trying to coordinate on building ambitious 'platforms'. Better to simply fund a broad range of independent research and see what emerges.
The project is organized into different divisions and measures have been taken to reduce the administrative overhead where possible. Having 50 small projects does not reduce administrative costs, you would still have an enormous amount of reporting, both financial and scientific to deal with (on the EU and on the projects side).
> And with no clear roadmap to guide priorities, that overhead won't provide any benefit
But that is one of the purported advantages of a flagship project. You do have a roadmap and a unifying goal that is provided by the project. Thus you can avoid different institutions performing the same research over and over without any concern to how this relates to previous results and other relevant areas. The difference is that the roadmap is provided by the project instead of the funding agency and as such there is more flexibility.
> building ambitious 'platforms'
To take one of the platforms as an example, the idea behind the brain simulation platform is to be able to aggregate scientific data collected one way or another (even outside the project) to build a simulation model. The more data collected the better the model. Then scientists can come and test their hypotheses or run scenarios. Based on the results the brain model may be adjusted. The way I see it, this will be an evolving tool that will facilitate basic research. I am not a neuroscientist so I can't really comment on whether this tool makes sense or not.