This is the hard part, for sure. Perhaps it should be a per-player setting, e.g. when you know the other player you can just turn it off and use normal human communication, but with random internet folk… :).
On the broader concept: I’d love to see a web-based implementation that was no more infringing than OCTGN but that stripped away some of the physical-space stuff that is inconvenient online, as @striatic said.
I suppose other windows are dealt with via the chat?
If you have any ideas I’m all ears 
I’ve been thinking about making a mockup of what I am thinking about in terms of a UI. I could potentially do more than think about it if anyone has any interest.
That’d be awesome 
I am interested
In response to the OP:
Yes!!! Don’t let the existence of OCTGN turn you away from building one of your own. The OCTGN version, while very good once you understand how to use it, can be very intimidating for new players.
If you created something similar to Dueling Network for Yugioh, but for ANR, that would be fantastic!
Making it web-based is the main draw for me here. If I can simply go to a website, log in and start playing, that would be great!
Or a more user-friendly client-based program, like YGOPro or DevPro, that would also be fantastic!
That is awesome! 
How would you see interactions work? Should there be a log/history? A chat?
still thinking about those things, along with the best way to display counters.
best way to display counters is actually on same card. im not sure showing status of ‘datasucker’ below it is good ui experience.
I reorganized things a little bit to give add a chat/log space, and to simplify the board by incorporating numerical values into the name area. + for strength, * for virus counters, ^ for advancement counters, $ for credits, ! for power counters. These could presumably become glyphs at some point. I think the most important things to display are the Name of the card and the modified numbers associated with it. Everything else is something that the player can remember, or check on by clicking the “card”.
The key difference between this and OCTGN is that by rejecting the card geometry we can pack things in much more efficiently and avoid overlaps that hide counters, make clicking things more difficult, running out of room when building large ice towers and so on. Serious Pet Peeves of mine with the OCTGN interface.
Here is a revision. Ignore the contents of the Chat box, just see it is there.
http://striatic.net/misc/Netrunner-Mock-Up-2.svg
Agreed.
For the chat/log I was more thinking something like twitch chat (ie. an area in the right/left hand-side).
Definitely 
this. Also I was thinking we could add a green/red overlay for modified values like in hearthstone when cards are buffed/damaged
Agreed.
This is awesome. Keep it coming
Oh, Hearthstone’s a good example, but also check out Might and Magic: Duel of Champions, it has a fantastic interface!
That’s what i was intending to show, just hadn’t added a text input box yet.
Possibly. There is an issue in that there is already a lot of green and red in the interface for displaying faction information. I’ve tried putting a little red or green marker on the side of buffed/debuffed cards.
Now that’s cool, seriously, you got something there that’s OG
For the overlay, I was thinking of adding the green/red to the number. That would mean that the actual value has been increased/decreased.
I’ve been thinking about the interactions and I see two ways of doing it
Unfortunately, this is not as simple as that. Some of the actions require more information (start a run on which server? break which subroutine? using which ICE? install a virus/ICE/asset/agenda/trap where? trash which cards?..). These interactions will require a more-or-less advanced modal.
Here’s a first attempt at listing basic interactions
* or use keyboard shortcut
I know this only covers the basic interactions but this is a start. What do you guys think?
yes. i understood that. it’s just that a red numbera on red cards and green numbers on green cards are less than visible.
I prefer this, although it would require a fair amount of space to display every option at once, all the time. Probably a matter of tabbing the chat/log with an “Available Actions” pane.
It could still be done via a list of currently possible actions.
In the situation in the Mock-up these would be the Corp’s list of possible actions.
and for the Runner, assuming it was their turn with the same game state:
That’s only 11 to 16 options each, in a fairly advanced game state. Very displayable. There’s also no reason why directing specific actions at specific servers needs to be very complicated. H,R,A,1,2,3,4 and all. Trashing during Install is slightly more complicated but is something to be handled after the Install action is selected along with a specific server.
For the advanced user everything could be done via Hotkey, or by some sort of shorthand command like “>p d[tab]” to autocomplete into “Play Deja Vu” or “>p i[tab] h” to use Inside Job for an HQ run or “>i s[tab] r2” to install Shadow to Remote 2.
The disadvantage of a pure Command Line Interface for a game like Netrunner is for the players to keep a mental picture of a complex board state without using some kind of ls command over and over again, but truthfully the number of variations on available actions at any one time is low enough that a CLI would be a very efficient way to play the game, especially with the ability to quickly reference a list of available actions.
Here are two revised mockups, using Red and Green “Buffed Numbers” - one showing a chat/log pane and the other showing an “Available Actions” pane with clickable actions.
Excellent!
I think they both are the same image though 
fixed.
I think instead of the buffed numbers, I would just make the original number go up.
Also, obviously it’s still in the early stages, but have you considered, instead of having the available actions on the right, have a menu that pops up when you hover over each card or section of the board?
Overall, though, it’s looking great so far!!