> 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.