Stuttering gameplay sounds like Dolphin's shader cache for the game is being generated. This behavior has not changed with 5.0, so all games can potentially stutter if the shader cache needs to be filled. Unless of course, you're referring to this kind of stuttering, as mentioned by the Wiki: "Higher settings and/or running in windowed mode cause frequent and annoying stutter". I can't comment on the lighting issues.
Out of curiosity, do the very latest Dolphin revisions (ones newer than 5.0) run Pokemon XD without these issues?
Out of curiosity, do the very latest Dolphin revisions (ones newer than 5.0) run Pokemon XD without these issues?