In case of "LED", yes, I saw that it is possible to create 1x1 LED Matrix and this is ok (anyway maybe it would be good to have directly something like single LED component) it is useful as visual indicator. But my main idea is to have option to select color - when you building big circuits you can use different colors to indicate some states of circuit. For example flags from ALU. I know also that there is output component which shows the value but visual indicator is sometimes also very useful.
As for T-junction I understand that it is some specific property because you always start from output to imput. For example creating junction is very anoying in LogicCircuit because if you want to create T-junction you need to click on wire with some keyboard button and then it splits the wire and you can connect other wire to this split point. The way which I like it is implemented in many tools like Altium Designer and LogicWorks - you can start by connecting components by any direction (you can start from output to imput but it doesnt create problems because still output is output and imput is imput, this is more editing behavior, I think). Or for example if you create mux with tri-state buffers you need to connect in some point two inputs to one output, ofcourse this works in DLS, it is just editing thing, in this other apps I could create wire from buffer to output and when I want to connect second buffer to output (with NOTed control input) I just start wire from buffer output and when I drop end of new wire to existing one it will create junction in this place.
It is described here on page 19: https://goo.gl/3pFqYY
And also on this image (the red dots are T-junctions):
As for RAM I think that it could be just simple device, I know that there are many types of memory but as always there should be some simplifications. Maybe something like this in LogicCircuit: http://www.logiccircuit.org/memory.html in this example there is separate port for data in and data out but in LogicWorks you can select if there should be input and output or bidirectional port.
If I will have other ideas I will write them here. Anyway your application is great and I thing that it is now the best logic simulator, also it is the only one with this "game" option which have great education purpose. If you will add option to add other languages I can help by translating DLS to Polish language (as I translated LogicCircuit). Greetings
PS: I created 8-bit CPU for my final thesis on my IT studies. Belowe there is partial schematic but it evolved much since this version (for example I added interrupts controller) but I was searching for app like DLS to create this new version so I think that I will soon to start building it in DLS, it would be 16-bit (I was thinking about 32-bit but I know that DLS is 16-bit max). I'm working also on FPU but I must redraw all of this in DLS because I was using LogicWorks before but it was too old and glitchy.