I will start off with an apology, I do not have much of an opinion to contribute to this discussion. I have already gotten the one Atma set that I care about, and do not feel strongly one way or the other about it's current or future state.
With that said, I feel strongly that any debate can be made more fruitful by having a better understanding of what the ramifications are of the decisions being made. Below, I have included a table which compares drop rate percents to the half life of a single Atma drop. That is to say, how many FATEs must be completed to have a 50% chance of getting an Atma.
This is a useful measure because it can be applied multiple times. Say, for instance, the drop rate is 2%. If you beat 34 FATEs, you would have a 50% chance of getting an Atma by that time. If you killed 68, you would have a 75% chance, if you killed 102, you would have a 87.5% chance, and so forth.
Based on what I have personally observed, and what I have heard from others, I would place the drop rate somewhere around 3%.
Code:
Drop Rate | Half Life
----------+------------
0.5% | 139
1% | 69
2% | 34
3% | 23
4% | 17
5% | 13
6% | 11
For those curious, this table was created using an inverse probability function:
1 - (1 - p)^n = H