The best quality frame rate increase using Twixtor

I'm sorry but I don't understand what you want to do. Increasing the frame rate speeds up footage. Increase from 24 fps to 48 fps and 10 seconds of realtime becomes 5 seconds of screen time. In this case, every other frame will be used. The only thing you might want to do when you increase the frame rate of a clip is to increase the motion blur. Frame blending will not do much if you want to speed up the motion. You would use Pixel Motion Blur or Force Motion Blur to perfect the clip.

When you talk about 25 fps footage and a 29.97 fps vs 30 fps I assume that you are trying to avoid any frame blending or minimize any frame blending problems. If you want to keep every original frame then all you have to do is change frame rate interpretation of the 25 fps footage to the frame rate of the sequence (Premiere Pro) or the Comp (AE). If your AE comp or your sequence is 29.97, which is the broadcast standard for all countries that use 60Hz power, then changing the frame rate of 25 fps footage to 29.97 fps (or 30 if you want) just means that 30 seconds of real-time will now playback in 25 seconds. The action will be a little faster.

If you need to keep real-time in the original clip then you don't change the frame rate, you pick the best frame blending method. After Effects and Premiere Pro have virtually identical frame blending options. For most shots, Pixel Motion is the best option. Pixel motion calculates the movement of the pixels and does a really good job of figuring out where the edge detail should be in the blended frames. Twixtor Pro has more options and can do a better job, especially when you want to slow down footage. The difference between Twixtor Pro and Pixel Motion is almost indistinguishable in a typical shot, but you may get some improvement in a shot with some really fast motion. Unless you are trying to create some extreme slow-motion where 1 second of real-time becomes 3 seconds or more of screen time, Pixel Motion will do a really good job of creating the extra frames needed for the slow-motion effect. I have Twixtor Pro and I rarely use it unless I need to stretch 1 second of footage to more than 3 or 4 seconds. It's just not worth the rendering time.

I believe AE and premiere use the same basic code for interpolation, but in AE, you can use the matte feature to help reduce artifacting if manually using timewarp instead of timeline mode. Also, there is no right or wrong answer because the framerate ratio depends on many factors such as how fast you are panning, what motion is in the frame, how fast the camera is moving in relation to the obect, and how smooth you want the image to be. 

In my testing (aka fiddling) I've found 50-80% the sweet spot for pre-comping, then timestretching the same amount to reverse interpolation.This gives you access to smoother frames while maintaing access to AE's matte feature. If you go this method, it's important to use whole numbers as truncating a fraction may not match everywhere and you may introduce a slight time change.