We probably should keep in mind in this folder that the audience is not ANR players
(me too, as I am guilty here as well)!
Putting on ANR hat....
Siphon and Noise mill became major problems in my opinion because there were interactions with other cards which weren't fully realized until the cards were in the wild. I agree that Siphon would not have been the same kind of problem had it been Criminal only. It was the ease of splashing it added to Runner having fairly easy recursion that made it a major problem. Likewise it was being able to "lock" R&D that turned Noise mill from just a major annoyance into a non-interactive nightmare.
Taking off ANR hat....
On the good side, these tendencies have not been present in the LCGs that FFG has produced more recently (AH:LCG, Conquest, AGOT2e). Instead, what we seem to be seeing is the Core sets contain moderately strong cards with each such card having a counter somewhere else in the set. The super powered cards seem to now come in the packs, which of course means they are subject to Rotation. I like this because it means the out of the box Core experience is better balanced which makes the game less likely to turn off an interested casual player who tries it.