Yes stamina and free throw training is important however with "new teams" I personally think the opposite. The reason is because a lot of the players in a new team are only expected to be short term players with only a few being long term type players. These short term players will most likely be sold since you would be aiming to replace them with better players. Therefore until you have a team that's more stable and unlikely to find big changes to occur with your roster then you should focus on training the skills of the better players in your team otherwise you will be throwing training away. Also money is important to new managers, if you train player skills up I believe they would be worth more on the market than if you train up stamina or free throw.
However I would definitely not ignore it once you have a more established team.
+1, i am also against the stamina and ft trainign for beginners they should concentrate on their valuable players.
I personal like training off position in the weeks where i just play scrimmage, so when i am a guard trainer i maybe play my guards as center/pf and train rebounding or Inside defence because this is the only time in the year you could do so without giving up games ;) One sweek stamina is often also a solution of wasted minutes, or maybe the possibility to play three matches hard in a week - and free throw when you reach level 3 you already shoot ~60% and the trainign ain't very valuable after this point with ft 7 you nearly don't see a different anymore with additional pops. So you could avoid training that, when looking a bit after it when you buy your players.