EDIT: Oh, and draw the otherwise skipped lines in 448/480 line resolution when the vertical window size is bigger than 224/240. You know, that thing that makes Sonic 2 splitscreen look so much better on Fusion.
Screen resolutions are being worked on. Gens/GS II currently enforces a 4:3 ratio for the visible area, but this will be an option later. Regarding 448/480-line mode, I do plan on implementing this. I did, however, implement "flickering" interlaced mode, similar to how it's done in Regen. Basically, it alternates between odd and even fields every frame. It isn't as good as 2x resolution, but it's better than only showing one field.
The pause tint is configurable in Gens/GS in the General Options window. Rerecording is something that may be done in the future, but isn't a priority right now.
It's been mentioned, and is planned for MDP later on.
Mega Mouse is partially supported in Gens/GS II. The protocol is implemented and mouse buttons work. I just need to figure out how to detect relative mouse movement correctly.