Intelligence influences how fast a player learns plays. They learn by repeating plays.
Some owners try using limited plays in games to speed up the learning process, but as you suspect, it causes loses due to play overuse. It's better to pick your top 40 plays, and let them learn them naturally.
I've completely changed my offense mid season, and it only takes a few games to start seeing improvements. You might even pull out a couple surprise wins, when your opponent is planning for plays you no longer use.