Well, nearly all the colour film I use is transparency, but I do use a negative film occasionally. Can't say that I've noticed any particular differences when scanning different colour neg films, other than Portra giving much better results (scanned or wet printed) than e.g. Kodak Gold.
By and large I find scanning from transparencies is easier - for a start there is no orange dye layer to mess up colour balance. I find noise is more easily controlled with transparencies. I've also noticed that scanned negatives need added contrast (consequent on the greater latitude), this can easily make things look unnatural.
If you know you are going to scan colour negative material, it would be worthwhile to try rating it a stop slower than its "official" value, as this helps drag shadow detail from the toe of the response curve onto the more linear section. It isn't likely that you'll burn out the highlights.