Every system has limitations and flaws. The trick is tailoring your system elements to serve your use case.

I've seen matrixed organizations (re)build themselves to Agile (multi-disciplinary) ad-hoc teams, where there are clearly some such teams that wildly outperform the others. Basically you just hope and pray you're plugged into one of the good ones. Meanwhile none of the lower-tier managers have any real control over workflow, workload, or what anyone is actually doing.