1. Six-year minor league free agents asking for $3+ million a year. There's a reason a guy is a 6-year minor league free agent! There are a few guys there that MIGHT be able to play for a rebuilding team, maybe a couple that could be bench players, defensive replacements, 11th or 12th pitcher on a good team. There's no one there who's going to be a key player on a good team. In real life, these guys are happy to get a minimum major league contract. Many will sign a minor league contract with a spring training invitation.
These guys just sit out there and waste, because nobody signs them and their ratings deteriorate until they suck so bad they finally retire.
2. Marginal ML free agents ask for ridiculous contracts. They get no offers, ratings start deteriorating really quickly. By the time their salary demands are reasonable, they're not worth signing.
3. No negotiating. Very few players - only superstars, really - have "take it or leave it" contract demands. In real life, a guy who made $2.5 million last year and starts out asking for $4 million this year settles for something between $3.25 and 3.5 million. If they're worth the $4 million, there'll be a bidding war that drives the price up.
Still enjoy the game, but every season free agency reminds me how broken some aspects of it are.