Rather than picking an and gate with 2, 3, or 4 (i think it's only 4) inputs you should be able to right click on the gate and hit add input (and obviously have a remove input option). Then in the basic gates menu have only a two input and gate.
Also the option of toggling the invertedness (sounds better than inversion) on each input/output. And then remove the nor, nand, norx, and nandx gates..
With memory (ram/rom/registers) there should also be two kinds instead of four of each RAM and ROM and then registers. One kind having multi bit inputs (address, data or just data for registers) and the other kind being like they are currently but with the option of adding/removing inputs/outputs.
Other than that i love how you can set the counting registers with several options. :)