I'm not an expert on emulators, so it's entirely possible someone has developed a solution (or I may just be wrong), but one possible explanation for cutscenes being pixelated could be if they are pre-rendered. If they are pre-rendered then it's just playing a video, which will likely have been created at a resolution to match the 3DS' screen resolution. So if you're trying to view it on a much larger screen, you obviously get pixelation. In that case I don't believe there's any way for anyone to fix it, short of completely recreating the cutscene :P
This isn't an issue for the actual game because the emulator can change how the game is rendering everything and swap out the textures for higher res ones. Some games do all their cutscenes in-engine in realtime, some rely on pre-rendered cutscenes and some do a mix of both.
Emulating hurts developers
by Thinking of you
Only if a platform is currently being supported by a company.
Besides the fact that the 3DS is on nonexistent life support, I suppose I could have mentioned that I own these games. I don't own a 3DS because I could care less about handheld consoles. I rather enjoy playing my games on larger screens.
How do you get past the touch screen controls? Are you using a game pad or KB & M?
On PC emulation, you use your mouse for the touchscreen. But I mostly play with my PS4 controller.