I think there are a couple flaws with the secondary position system that aren't exactly pressing, but could be addressed in next years game. The biggest issue is that when playing a secondary position the fielder only suffers a minor hit to their attributes; the problem with this mostly deals with catching. Carlos Santana, for example, can catch just as well as Yadier Molina because of his secondary, even though he was moved from the position over 5 years ago. Kyle Schwarber is similar.
It extends beyond catcher though. Rhys Hoskins, the worst left fielder in the league by a mile, can play bronze defense there because he is an average defender at first. Ryne Sandberg, a gold glover at 2B but an average defender at 3B irl, is just as good as Arenado at the hot corner.
Stemming from the first problem, secondary positions are handed out too widely. Schwarber and Santana would not be out behind the dish in any situation today except for an absolute emergency. Similarly, Mookie Betts would never play 2B except for an emergency, yet you will see him played at 2B playing top tier defense the majority of the time (he's made 2 appearances there in his career).
In any case, I think there is a rather easy solution for this. Instead of giving players secondary positions a slider system could be implemented to rate their ability to play each position. To use Santana as an example (who has 1B as a primary and C/3B as secondary's), he would have 100% at 1B, meaning he would suffer no penalty playing there. But his rating at C could be 50% (or insert any number variable here), a recognition of the fact that he wouldn't play defense at the same level as first base; the same would go for 3B. As for the rest of the positions, he would have something like 10%, showing that he could barely play them. I think this would give more flexibility to secondary positions while also making it more realistic, as you can detail how a player plays at specific positions without making them godly fielders.
TL;DR: A slider system should be implemented instead of the current secondary position system, as it would allow for a more realistic depiction of secondary positions.