Make Chemistry have a more tangible impact on your teams play so you can not get away with ignoring it.
However, there should also be more ways to increase your teams chemistry like two players playing next to each other in your line-up should continuously be improving their chemistry.
example: Two guys with low chemistry because they are from different league and different countries that play in your line-up next to each other should eventually have the potential to have perfect chemistry. Imagine they play 500 games next to each other they will over come the chemistry issues.
And add consumable cards that increase the chemistry between two players.
You could also have stats that increase the chemistry between them like one player assisted the other. Or a 100 completed passes between the two players etc...