Yet Another Hacking Overhaul

Lack of transparency. Even after tutorial and many games with the system the best players still cant tell you what works and what doesn't.

I personally went into the expansion and started toying with the mechanics, did not play the tutorial, and I personally found it fairly understandable. In general it is rather straight forward, and I quickly understood that hacking from futher away is safe but slow and choosing origin and targets systems close to eachother sacrifices that safety for speed. It could definitely be better guidelines in place, but its not that hard or obtuse. The only thing I personally would like to complain about is that there are no indicators, unless I am blind, of your planets harboring Sleepers even though they are clearly visible when hovering planets which just seems silly to me.

Lack of useful programs. While there are many programs to research and develop, not a single one seems to have any impact on you or your opponents. While that may be a symptom of problem 1, I do think that it was possible to not have this problem, while also having the lack of transparency.

This is can somewhat agree with, personally I have come to only bother using defensive programs in nodes I know are exposed, or are entry points, and my capital. I also find that I only use offensive ones when I play the Choir, as alot more time and importance lies in the hacking, and then usually only the one to increase hacking speed through a single or multiple nodes.

Lack of counter-counterplay options. In mid game it is pretty easy to get your Approval to 125%, then activate sleeper removal on all your planets. As long as you remove all sanctuaries from the planets, UC can not move into your territory unless they go to war (and they are really bad at it).

I do agree there should be ways to combat your enemies' measures to you, but the Sleeper removal action being 'free' I feel is a reward for those who focus on Approval or have amassed the influence to apply the Saints & Sinners Bill. I'd much rather see other solution - just off the top of my head, perhaps a tech that allows the creation of two sleepers or something. 

Minor flaws. There doesn't seem to be a reason for levels of hacking outcomes (except for one Defensive program). The trace mechanics are too simple, yet very much not explained. Unlike Behemoth techs, hacking is localized in the bottom research quadrant.

Agree on this last one, the Science quadrant should perhaps facilitate your own hacking and direct counter measures, but, for instance, the Empire Development quadrant could give access to buildings or actions that shield from potential hacking attemps and/or outcomes.

Given that, here is my idea for the hacking overhaul:

1. Offensive programs are now Operations and hack outcomes.
2. No more limitation on active operations (except for Bandwidth).
3. Current Offensive programs are now Utility programs. (unless you will want to remove these)
4. Defensive programs now define trace speed and trace outcomes.
5. Programs (especially Offensive programs) are now spread around all the quadrants. Programs in Economic quadrant effect economics, in Military quadrant – military and so on.
6. Bandwidth buildings.
7. Scaling penalties for searching for sleepers.

1. Think I agree with ThantosArigata here, that it might cause problems to choose the outcome before succesfully hacking something but, then again, that could be a layer of risk. 
2. I personally like that Hacking Operations and Bandwidth is seperated, and would rather them add more operation slots available through research or whatnot. The reason I like the disconnect is because I feel a purely Bandwidth restricted system would far too heavily favour huge, sprawling empires with tons of Bandwidth buildings (yes a spoiler for point 6) and/or the Choir. And while, of course, the Choir should be the best at hacking there should be limits. 
3. Sure, seems alright. Fewer buttons to press is always good in my book.
4. Sounds great, and perhaps we could even have more outcomes.
5. Makes sense to me, thumps up for a Program that converts a Pop or Sleeper into Essence.
6. Yes! We need this! It would enable non-Choir empires to at least come close the Overmind's hacking skills.
7. Already touched on this, but I see no reason to make penalties harsher. But there should still be counter play if you invest resources, like the aforemention Saints & Sinners Bill could make Pops immune to becoming Sleepers or the Larger Hosts Bill could periodically converts Sleeper pops to manpower.

Interesting ideas, for sure! Personally I do not mind the system as is, but if these things were implemented in a thoughtful manner it certainly sounds like an overall improvement, especially for the Choir as it might make them more interesting.