For 1.5, I'm just working on a patch that lets you hide all labels at once and probably also saves the settings (whether the labels are shown or not). The former might even go into some future version of 1.4 (the latter not, because it entails a file format change).
Yeah, however it is not just the label, but the indicator line as well that makes the different (and unpleasant to read on the screen) line spacing. How about moving the indicator line a bit further up?
For representation issues, I'm also thinking about adding preview-latex facility to character styles. That would give you a wysiwyg impression of how the output will look like.
That would be cool! It would be even more cool, if it was optionally possible to represent the character class *only* via the preview-latex setting and leave out the indicator line and label. That is, to define something that is presented on the screen with a similar user experience as the current text styles (Emphasis, ...) . Another issue with the current inset-style implementation is that it always appears on the screen as if there were an extra space at the boundaries. If one assigns a character class to same chars from the middle of a word that looks quite odd.
All in all, character styles are still very much in development.
Hence, it is the right time to be a bit picky about details ;-) (I really appreciate the effort you guys are putting into Lyx!) Daniel