I'm going to go to my usual soapbox and ask for admin tools.
There's almost no change to the game engine in terms of balancing that won't be tested and exploited given enough time. Rather than going through an endless series of buff/nerf cycles from a development standpoint to counter this - a sequence that can never be conclusively won - instead give league admins the ability to affect player performance on the field, and the make-up of new draft classes.
What could be controlled? The effect of play scouting could be amplified or reduced. Increase the overuse penalties. Add overall offense or defensive modifiers to all stats on underused plays. The more, the better. Feel like the HB flare needs toning down? Slap it with a -10% offensive performance modifier. Want to beef up FB dives? Give them a -10% defensive modifier. You could be even more granular, modifying individual player stats on a per-play basis. An insane amount of work for admins to do, but they're already investing a ton of time in keeping leagues entertaining, competitive, and fair.
Want long passing fixed? Easily done with a few modifiers.
To test these modifications, allow admins to run the play repeatedly in a test environment using standardised players. We'd soon reach a situation where every custom league has its own identity, also enabling every era of football to be better replicated. Instead of players sharing optimum weight settings, thereby making the game head in a cookie-cutter direction, instead you'll have admins sharing optimised play modifiers.
When it comes to incoming draft classes, give admins the ability to control the ranges and scarcity of stats by position. You could set it with such granularity that every player in a given position has identical stats (effectively giving the opposite game to "roster only" - "gameplan only").
Further, it would then be beneficial for admins to be able to set default position weights for the league.
There are two keys to success. The first is transparency. Balance changes could be limited to the off-season only, and then any change to the league settings auto-posted to the forum (as they are with trades).
The second is flexibility. The more power there is to change how the game performs, the more each league can take on its own identity, the less power any overall meta has, and the less work needs to be done on the dev side to offset exploits. I, for one would rather have more features and more plays added than all dev time being spent on fixing the latest overpowered play.
The normal counter here is "but what about unscrupulous admins?"
My response is straightforward: watch a bad admin try to persuade people to join their leagues. Anyone rigging it in their own favour will find themselves playing against ghost-teams pretty fast.
Fundamentally, this takes the responsibility to constantly balance the game out of the hands of one developer, instead giving it to the league controllers so they can create a better experience for their team owners.