You have indeed 2 options for rednering Vue elements inside C4D: either automatic, then most render parameters inside Vue are set to match C4D render settings, whenever possible (max ray depth for example has a maximum of 7 in Vue if I'm correct, so if you have ray depth to 15 in C4D, you won't have more than 7 in Vue anyway), also texture filtering and texture anti aliasing are not matched, there won't be texture filtering in Vue unless you use separate Vue render settings.
Now if using Vue render settings, you can access all presets or create your own render settings for the Vue parts. Using your own render settings will allow to fine tune the texture AA and texture filtering, needed for animation.
Please note that object anti aliasing is always done by C4D, and maybe this is where your problem lies.
If you have AA set to "geometry" in C4D, then the AA quality of the Vue elements will be bad, even if using high Vue settings, because the plugin doesn't deal with AA, it lets C4D do it so AA levels are consistent throughout the whole render. So you'll need to set C4D's AA strategy to "best", with min1x1, max 2x2 to get good AA levels on the Vue elements, even if you wouldn't need such levels for the C4D elements .I rarely use "geometry" anyway, it's not good as soon as you have a Nurbs object in the scene, but sometimes, it can be enough. But if you have Vue elements in the scene, you'll need to use "best".
Let me know if this fixes your problem.