i doubt there is anything in the game to prevent what you described, it is usually detrimental to move a stronger player to backup, and a weaker one to starter, so that is probably what you were seeing.
i fairly often will not start my best 5 players though, if i have more than enough offense on the starting lineup, and a backup line that could really benefit from one of my top offensive players. then i will move a strong offensive player (preferably weaker on defense) to the backup spot and he will usually shine in that role, facing inferior competition. it costs you some minutes, even if you play him as backup at 2 spots (which also seems to put him against the stronger players more often), but i think its worth it. especially in an offense like triangle where going from say 3 dominant offensive starters to 4 has small benefit, but adding one to the backup line is a huge bonus.
the other way to play it is to intentionally sign a guy to be a career backup, who is fantastic on offense, but i generally don't go that route. not sure why, it can be extremely beneficial if the guy is really good on offense. one of my most productive players ever, who lead the team to a couple titles, was a d2 guard with like 92 spd and 99 per who never started a game - which i expected when i signed him. but he was the leading scorer for at least 2 years and was 1st or 2nd as a soph (redshirted). his poor def and pass made him a poor choice at starter but i never regretted him once (i think he was also in a big class, which helps, i probably started a junior ahead of him as a senior but other than that he was never the natural choice, just based on age alone).