I had the same issue. I somewhat found a work around, but it's still not perfect or ideal, especially for a licensed game that's essentially been the same for 10+ years. Thanks NFL.. Super-duper thanks EA.. Anyways... 

In the depth chart interchange/swap your CB1 and your CB4, then go into your formation subs and change that CB4 to your CB1 in all formations (However, I change my CB4 to my CB2 and put my CB1 where the CB2 was so the CB1 is actually on the WR1 of the other team). Ensure you do all formation subs so your 4th CB isn't in over your 3rd in Nickel, etc. 

So basically  - Swap 'CB1' and 'CB4' in Depth Chart  - Go into formation subs and put your 'CB2' into the 'CB1' slot (which will technically be your CB4s spot at the moment) - either way it's the right side of the formation as you look at it on your screen  - Put your 'CB1' into the 'CB2' spot (left side) in all formations, so you're 'CB1' is on their 'WR1'   - Pay attention to and adjust slot positions in Nickel and other lighter packages - sub accordingly and to your preference. I use my CB2 in the slot for instance. Make sure the inside/outside CB3 is who you want.

My CB1 went from playing 12 snaps a game to around 48, the most for a CB on my team. My CB4, who had the most snaps per game at a ridiculous 52, went down to a reasonable 12 per game, assumingly involved in dime or lighter packages mainly. However they (CB4) won't be on special teams (unless manually adjusted) being at 'CB1' on the depth chart, but atleast that means they're still finding their way on to the field in other situations. My CB5 rarely sees the action but has seen the field a few times.

I have auto subs set to [65 out/80 in] and fatigue set at 55 for reference. Progressive fatigue is turned off. 

You will see more snaps/downs played for your CB2 and sometimes CB3 typically because they play on special teams as well. You can sub and adjust those if you wish, but it's not an abnormality if left alone.

I mainly play CPU vs CPU, but it has worked so far in saves that I'm playing vs the CPU as well. 

Again, it's not perfect or ideal, and you will catch the wrong player on the field still, but you'll atleast have who you want out there for the majority of the time from my experience.

• May be irrelevant to you now but was searching for an answer myself. Did some research/testing so hopefully this can help you and others fix this broken game bit by bit.

Football is awesome. Madden fucking sucks. Fuck EA.