I just came back from a holiday trip and a few days off to notice that the game interface has been switched. It looks like in my ignorance I have missed hearing about this before it actually happened. I hope it’s not too late to still give feedback 
I’ll start with the “likes”.
I like the little puzzle icon on the top left, before the name of the puzzle. I also like the total energy display being under the requirements rather than being left from them.
I like finally being able to copy a sequence into a puzzle, no questions asked. This is probably the one reason I’d keep this interface compared to the old one despite the list below…
I like the option to turn chat off altogether. I’ve been using that “hide chat” arrow quite a bit lately… The only problem there is not being able to help those that need some and ask in chat. Would it be possible to create a “small talk” channel? =P
Now, on to the “indifferent”.
I’m not entirely sure whether it’s better to highlight the red parts of a shape on the actual puzzle or to enlarge the shape icon. Experience will tell, I assume. It’s an interesting idea for sure.
Finally, the “dislikes”.
The icons for the pair requirements. While they contain more text, they do not contain more information. In fact, their information value is less. This is because the actual pair icons are not straightforward, and smaller than they used to be. It’s not the full icon I’m talking about but the 2 colored circles inside that icon. Which is the information. The base circles should be bigger and should also be closer together to more amply represent a pair.
The same goes for the number of these pairs. The number we have is arguably no more important than the number required. Either way, the information is the numbers. The text “more than” and “less than” would really belong in a tooltip. The colored numbers in the old interface did a much better job in representing the information about the amount of these pairs.
The total energy of our shape gets lost with the small, normal typeface font. It’s much more important than this display would indicate. At least in the game, it is…
While the camera icon for taking screenshots is better placed in with the other buttons, the popup now does not underline the word “this”. This means that the player has no indication that the screenshot is viewable and is not solely for linking into the chat window. It may also be pointless to ask this question with the chat window turned off. It could be better to have something along the lines of "Your screenshot can be viewed here: ", and then, depending on the state of the chat window, either a simple “Ok” button, or a “Would you like to post it in chat? Yes/No” question.
The Natural mode / Target mode selector should have a better, more informative placement. The icons themselves are not very representative either. True, a leaf might associate to nature, but as long as the energy model itself does not mirror that notion perfectly, I would stick with the circular double arrow. “Target” is also more like a bunch of concentric circles without the actual arrow implying what it is.
The pair selectors, along with the way they are highlighted, are horrible, compared to the old setup. Both the information content of the icons, and the informational value of the highlights, are less, than what they used to be. Add to this the bad placement they are now in for a complete catastrophe.
In general, the most likely area of the sides of the screen to be covered up by a shape is the lower middle. Before now, the only buttons there were the less important ones. Even if the buttons were made to “stick out more”, it would not help the current situation. The more important buttons need to be elsewhere on the screen. I would consider this to weigh a whole lot more on a scale than the “tidy look” of having all the buttons together in a single line.
The Undo/Redo buttons also have this problem. Previously on the edge of a panel of buttons, they are now stuck in the middle. My guess would be that the person who designed this interface uses a huge screen and doesn’t like having to mouse out to the sides. This would explain why all the really important buttons ended up in one batch in the middle.
Unfortunately I don’t think that this makes playing any more efficient. Input is only one side of this coin. The output needs to match that efficiency. I don’t think it does with this particular GUI.
Even if we do stick with the idea of having all the important buttons in the lower center of the screen, I would still recommend at least a few changes. In particular, the less important buttons (zoom in, zoom out, options, screenshot, copy, paste, and reset) should go someplace else. I would still go with moving the important ones instead though. And not necessarily in one neat, streamlined line, either.
Last, but not least, I never liked the huge “MISSION” highlight of NOVA. I still don’t. It’s a pointless reorganization of information to display an arguably cool image. It separates one, supposedly more important (???) goal from the rest of the objectives (“Your RNA must fold into the target shape”, or, as it says now “Match the desired RNA shape!”).
At this point, I can’t help but feel the need to apologize. I really should have said all this when I played through NOVA. At the time, I was under the (obviously wrong) impression that it was a sidetrack. Not a glimpse of the future. I just hope that, now that that future is the present, it is not the end of the line.
Obviously most of what I said here also applies to NOVA. I assume that from now on it will be just the one interface, so any changes here or there will apply to both.
Edit / PS.: Oh, and sorry for not posting in the feedback thread, I saw it before posting, and now I’ve read it too, but it’s pretty much all about lab stuff. This isn’t. This is about “look and feel”.
Also, I have since spotted that structure energies are displayed next to the total in their own separate icon now (on mouse over a structure). I like this idea, but it would be better to elaborate from everything being either a loop or a stack to something more explanatory. Without that, this information is not very useful. Not that it is otherwise, at least not with energy numbers turned on. It’s nice to add up the quads to get the total stack energy but I have yet to see a situation where this is really useful.