My biggest issue with Linux Non-linear video editors is that all the ones I've tried seem to process video and audio independently. I have lots of video that for various reasons may not have perfectly aligned audio/video. These play fine in most players (since the proper timestamps in the stream allow the decoder to align them) but once run through an editor, the streams are misaligned. Generally, it isn't something as simple as apply an offset or scalar, so there is little I can do.
Another of my desires is a near-lossless editor which could cut and splice videos only re-encoding the necessary frames (generally the missing reference frames) while working with H.264 (or equivalent) codecs.