I believe part of the issue is the "pay to play" situation that's been created and perpetuated by these institutions. These well established companies have deep pockets and therefore the ability to invest in powerful tools/instruments (not to mention the space to store and utilize them) which means if seasoned and budding scientists alike are interested in practicing their craft for some pay, they must do so within these institutions. Obviously, as your post states, these institutions will want a piece of the pie for providing these tools and their facilities. Thus the cycle will continue on until we've figured out a different paradigm for pushing forward science while better rewarding the people doing the work.
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I agree totally with your statement about access to tools and instruments BUT very shortly we will see a big drop in prices thanks to technological progress. That might change the game completely and this monopoly might be broken up. Here is an example http://newatlas.com/home-crispr-gene-editing-kit/40362/