John,
I have a home-theater set up that uses the full-size Ohm 100S3's for LCR, a half-size sealed omni version of the 100S3's for left and right surrounds, and micro-Walsh shorts (not omni's) for the rears.
As far as your questions, ...
WAF: I do not have the wall-mounted versions, but my wife thinks that the micro-Walsh's are cute. Also, hearsay says that WAF is highest for wall-mounted speakers.
Wall v. Short v. Tall: I am assuming that you are going to play movies, so that you will need a subwoofer (even if you went entirely with 2000's). You will have more flexibility on the crossover point as you move from wall to short to tall. The other consideration has to do with the fact that your couch is against the wall. This means that you are relying entirely on your surrounds for rear envelopment. The short/talls might give you more flexibility in placement as you try to get the right sound. For example, I think that omni's disappear better when they are out from the wall a bit.
Muffling: This is more important for music. In home theater, as I understand it, surrounds and rears are used mainly for short-duration localized sound effects and diffuse ambience. My understanding is that film-makers do not want those speakers to produce sounds that will induce listeners to turn their heads away from the screen in response.
Height: For movies, most recommend that your set up support the reasoning given above in muffling. The majority suggest that tweeter level be at least one foot above ear level, but I have seen people say to put speakers on the floor and fire upwards, to fire them into corners, etc. I have my surrounds and rears up on furniture so that they are about 1-2 feet above.
Center Channel: I am of the opinion that a dedicated center channel speaker is preferable to phantom imaging. If you are going to use phantom imaging, you can't beat Ohms because of their wide sweet spot. Still, I have found that phantom imaging tends to make it seem as if someone's mouth is several feet wide. I also think that dialogue is more intelligible when given its own speaker.
Finally, remember that Ohms are not the "loudest" speakers out there. This means that you should not expect to be able to play at reference levels (105 dB non-LFE peaks) even with gobs of power; if you try, you'll just burn up the super-tweeters. I find that -10 dB's is about all I can hope to get for a listening position about 10-11 feet from the mains.
