Build governments and your coercion problems should go (at least partially) go away.

  I find it annoying at game start that you get a 1% penalty at 45/45/10 and a 10% penalty if you use the focus on top of this.  Makes foci useless in the early game, and requires a messy 44/44/12 to avoid the penalties.

  I also dislike that there is no warning if you are getting coercion penalties.  Took me a few games for me to even see the pop up on the penalty to raw production when I used focuses.

I believe it is an intended challenge to make up for the power that is wheel and focus management.  I don't know what the governance techs do exactly (which is a different and troubling issue), but they seem to help.  I very much hate the coercion penalties and go out of my way to manage them.  This is, to me, a successfully challenging mechanic that impacts my early game and colony rush.  It also shapes a lot of my late game now.  I really enjoy working to meet that challenge and get the best out of the present system.  I am hoping they find ways to link it to a couple other mechanisms and really integrate it into the economy.

Coercion is a percentage loss of your base production, and you can impact it in two places.

• Open up Governance tab and play with the wheel in there that sets priorities for all of your star systems.  If you set it too heavily in one direction or another there can be a massive loss of productivity.  My most common setting is 44-44-12 Manufacturing-Research-Wealth, which gives me a coercion penalty of zero.  
• When looking at a planetary screen, you can also set priorities for just that individual planet.  For example, to divert resources away from manufacturing and towards research.  if you do soothes will also apply coercion penalties against that planet, you can easily see this by looking at the total productivity.

Lesson:  Focussing too much is bad.  Your people don't like it.  

Additional point, Coercion also affects Morale by the same percentages.  You will see it listed in the hover tips for both Production and Morale in the planet govern screen.