After reading through this thread just so new players won't be asking for stuff that everyone else asked for I'll just summarize.
1) A System like RAM thats replaces the program libraries
Waiting around forever isn't really fun and although we do acknowledge that it takes time to do certain things we would rather prepare for when we feel like hacking. Its just like buying groceries and putting them in the fridge for another day.
If the current program libraries were converted, I would rather have it be like [Level 15 Program Library | RAM - 90 | Disk Space - 180]. To balance it a bit I would also add a transfer time that decreases with the level after all it takes time to write files to RAM on an actual computer.
2) A Buff to Stealth
I've noticed as you level up higher, hacking in full stealth is practically impossible. Because of that it's either a full brute force or a hybrid hack. Feel free to correct me if I'm wrong.
A node called the "Encryptor" to increase the amount of time you could spend in a stealth hack (from 3600) would really make stealth more viable in higher levels.
3) Base Building and Testing
Many people have asked for a test your own base feature. This will not just improve the difficulty of bases, but allow for users to learn how the game operates and not just through the tutorial and missions. From personal experience, I normally make a base setup and then nobody hacks till I levelled up into a new rank where parts of my base isn't effective anymore. A system like this can be very game changing and should be limited to something like three tries every time you relocate more than 5 nodes which would be compared to how the base was before. This is also another excuse to ask for the ability to save base layouts.
4) Getting players to Hack Other Players
Even if you force players to hack someone if they normally don't, they would just pick the easiest base. Having other players test your base is more important than testing your own base in my opinion (even though I want to be able to test my own base). Other players sometimes find ways to get through your base that you haven't thought of yourself.
Unlike the others I'm not just going to ask for a "test my own base feature" but a bounty system. Why wouldn't a hacker with a high rep get a bounty put on his back? This way players with a high rep and no resources wouldn't just lose their rep just to get more resources especially when the targets on their map have big bounties on their backs. The bounty should also increase the more time a player wasn't hacked.
5) More Nodes
Some others have asked for another attack node that takes after the "Shuriken" program or the ability to build you're own nodes. For defense nodes I would rather have a generic node and by assigning a program to it, it would then take a bit of time to convert (depending on the level). Reserving worms for the "Sentry", the "Blaster" would make the turret into a "Black Ice". Programs that are unlocked later on in the game like the "Maniac" would be quite interesting to see how players use it considering that it's a one time use although it would be weaker than the actual program.
6) Attack Priority
One thing I have spotted and it kind of bugs me is that when attacking and you have a node in your control and you attach a "beam cannon" to it, the cannon will attack what it wants, however some times I'm sat there wishing I could tell it to attack something different.
Like CovertHoax's idea for "Malware IDE", telling the programs what to attack first and/or being able to switch what they attack during the fight (with the target change delay factored in). If no input towards this is given from the user, just follow the regular attack priorities.
7) Offline Base Section
This idea would follow how "Twin Ergos" mission is laid out. With an offline-core, nodes like the "Converter", "Safe" and "Scheduler" plus two slots for regular nodes may fix what many players complain about.
The "Converter" would be where players convert their Bitcoins into money with a bit of a conversion loss and waiting time.
In this case, as you upgrade the exchange rate/fee should go down with each level. Or maybe a limit to the number that you can exchange, which increases as you level up. Something like that.
The "Safe would be "a limited storage that stores a percentage of the maximum resources" was my old idea but I've realized that treating it like a smaller "Database" would be better. Or just allow the offline-core to have "Databases" and "B-Coin Mixers" but at far lower levels.
The "Scheduler" would be in charge of controlling "Building Threads" and "Compiler" so the upgrading building can be upgraded in the least amount of time. For the building threads we should be able to disable this and for the compiler this could be built in as a cheaper speed up button using credits under "Optimize".
8) Randomly Generated Bases
These would pop up occasionally during gameplay. These could be a way for the Devs to test new features and for players to gather experience.
Hackathons would consist of a base that multiple people would hack in order to see who could get the most points in one try. The brackets would be decided on by level and reputation just so a new player isn't put against a seasoned veteran.