Yeah, OK, so they did technically release a live version as a single in the interim period between Fish's departure and Hogarth's arrival, but it was a b-side first, and thus it still fulfills my promise. Look, this one has to go hand-in-hand with "Separated Out", because it's basically the Fish-era version of the same song, and a comparison of the two makes a nice microcosmic comparison between the two eras, which seems like something I ought to do, right?
The most immediately striking thing is that the keyboards are far, far more prominent here than they are in "Separated Out", despite that actually having one of the more noticable keyboard parts of any post-EMI Marillion album. Mark Kelly doesn't get to stand out a whole lot in more recent albums, which is not to say he isn't still a totally essential member of the band, of course.
Another obvious difference (which you can see for yourself with my handy lyrics links, aren't I great) is that there are a lot more words used here to bring across the same basic point. Not to say that Hogarth (and Helmer, from time to time) don't get very wordy sometimes, but Fish will never, ever use one word when he can use twenty five. Sometimes this interferes considerably with the clarity of the point he's trying to make, sometimes it makes for fabulously erudite poetry. This particular case falls somewhere between the two, I think.
Further to that, there's a contrast in the tone of the lyrics; while "Separated Out" is all questioning; "Am I enough of a freak to be worth paying to see?, "Freaks" just comes straight out and cries "Please stop staring at me". Either way, they both refuse to sit straight and shut up and become accountants, as would be the sensible option if you wanted to avoid the stares, but the difference is telling; Hogarth-era is definitely characterised by a much greater openness to positivity, even if it doesn't always fully embrace it.
Of the two, I think I enjoy "Separated Out" more, but I may be biased towards it having seen it live; I imagine "Freaks" would have much the same improvement. That last sentence pretty much still works as microcosm, by the way.