Yeah I've said before I'm anti-Brown so I won't go on too long a diatribe about him, but undisciplined basketball is sort of his hallmark. Your #3 point certainly played a big part in the latest meltdown (O'Quinn, Korkmaz with very efficient first half numbers, barely get to make an impact in the second with O'Quinn not playing at all).
My #1 thing still is the lack of development of young players. Just Embiid has really been the biggest shining star, though he seems to be flawed with his conditioning and I'm not sure he won't break down in the playoffs like last year. Korkmaz has been pretty good so far, so perhaps he's finally developing when given a chance.
Simmons is still what he is -- a good regular season player who puts up numbers and gets you to the playoffs, but if he keeps up the non-shooting stuff (which Brown condones by playing him and not taking away minutes), this team will be shut down in the playoffs. He's a liability on the offensive end when facing good teams who have the personnel to shut him down, and this team as constructed has less to counter that than previous years (less shooting, less spacing). I'm not a believer Ben will ever change.
Long story short, last year was probably the best shot for a ring.
Good news is the season is still young, and the team has little cohesion, so that should only get better as Richardson / Horford get used to playing with the rest of the team. Even without the cohesion or the team shooting paricularly well, they've been in most games. The bench, which I thought would be a weakness (though I wasn't against any moves they made given how they went starter-heavy), actually may be pretty decent.