This is exactly my point. Say you lower the penalty to 15%. You would actually be able to make pretty good players. They won't be as good as if they were trained with 1-position training, but they would be good enough to contribute, especially at lower levels.
- you get 6 players which look the same instead of 3
I don't see this as an issue. If you only have use for 2 of them, then you just sell the other 4. This would mean more players on the transferlist, and the manager would have money to buy players for the positions he hasn't trained.
- it takes longer to get to the same skillset because the training is slower
- you need to sacrifice 2 positions for training instead of 1 (2 guards for OD or PA, 2 big men for ID or IS or SB), making it harder to compete, because you need to hide 2 players on defense instead of 1 and you need to play a big man at a guard position or play with no flow
- you won't be able to cap higher potential players (i.e. the ones that will help you in higher divisions)
Well since this thread originally was about new users, this might not be that big of a problem. You don't need to cap high potential players at the lower levels. Capped starter/star/allstar potential players will do the trick. When you then need the higher potential guys you can switch to 2-position training, but that is a managerial choice which, in essence, is what this game is all about.
Increasing 2-position training speed would be a way to make new managers see progress faster and it would increase the number of mid-level players on the transferlist, which is what the OP is asking for.