On the topic of retention, games in this genre aren't super popular because people usually like to feel like they're controlling their performance. This game does a good job of alleviating that by having a customizable ruleset, but the default game plans and player weights are straight-up trash. There's a very steep learning curve, plus a new player can join a league with experienced owners and get absolutely stomped on for a couple seasons before giving up. And this is the real issue with retention -- it's very likely that new owners will spend their first few seasons getting the **** kicked out of them by experienced owners, rather than competing against other similarly-skilled owners.
On the topic of game planning, the main issue is the lack of actual customizable plays leading to a playbook filled with mostly bad plays and a small list of "premium" plays. New owners are presented with a large playbook without any real direction on how to formulate a game plan, so they often select these trash plays that wouldn't work even with the best roster against the worst roster. Experienced owners have had time to see which plays are good and which plays are trash. The inability to use long pass plays (due to the high effectiveness of a 4-man rush) is 0.4.6's biggest flaw, since even many of the medium passes do a great job at punishing OLB Flat Zone spammers.
With the 4-man rush able to continually create sacks on long passes, unbeatable strategies emerge. To wit: flat zone + run keying, or blitzes with pass keying. Flat zone destroys short passes (a key element of winning in 0.4.5, which is why flat zone spam was the first meta in 0.4.6 ), and blitzes destroy everything else. So this leads to 3 kinds of defenses: flat zone spammers, LB blitz spammers, and clueless owners who play zone. Flat zone is beatable by certain runs and medium passes (long passes would be great if they could withstand the pass rush). LB blitzes are beatable by short passes and outside tosses, especially those with RB flat routes. And zone coverage is beatable by basically anything (except long passes, which are unusable due to pass blocking deficiencies).
The end result is that there are currently about a dozen owners who use only premium offensive plays and one of the two main defensive strategies, and many others who are starting to copy us. As more and more people have figured out these premium plays, parity should increase. However, those who figured out premium plays early tend to be those who have a better understanding of roster building and player valuation, so that advantage still stands. So we've ended up where we are now: new owners get turned away by getting stomped by experienced owners, and experienced owners lose interest from the lack of variety in strategies.
With this perennial advantage to experienced owners and emergence of a small set of winning strategies lacking in counter-play, most newer people quit. New versions of the engine can fix the counter-play issues at the top level of competition, but new player retention will continually suffer without opportunities for them to feel successful.