2) I have asked to join ICGA investigation panel just to make sure evidence is objective. Indeed it was objective and you made a very good job. However, my only concern was about the evidence itself and I am indifferent about the verdict. You have looked at R3 internals and you are one of the very few persons in this world who could say that it is (almost) clean from fruit origins, yet you remained silent... strange...
I mentioned briefly in B.2 of RYBKA_FRUIT that R3 had a re-written evaluation function by Larry Kaufman. Beyond that, I don't think anyone really brought up R3, except for Bob saying that R3 might have Crafty bitboard code. There was an occasional comment as to whether R3 should be investigated, and the general consensus was no, as Rybka 2.3.2a sufficed for showing that a world championship was won with tainted code [and most Panel members probably didn't want another reading assignment

], at which point the ball would be in Rajlich's court. The fact that R3 was/is not freely available also played a minor role.
If I had thought that the majority of the Panel was mentally assuming that R3 was also overly Fruit-like, I might have said otherwise [though I'm not sure I would have been willing to invest a lot of time to write a convincing document about it] -- but given the (well-known) LK/evaluation situation and (say) Don Dailey's opinion in the Report [also Gerd's, though I think he got the date of Rybka 3 wrong], I didn't think this was the case. Also, I can't say that I agree with (say) Mark Uniacke's opinion as quoted in the Report regarding later Rybkas, but then I'll let him speak for himself.
1) I fear that I had mistreated Ippolit for a long time without looking into R3 myself. My 'prejudice' was mostly based on your R3/IPPO comparison paper. Now I am almost convinced that Ippo was indeed written from scratch - and is completely legal. I still think that most of ideas were gained through RE, but this is not illegal in any way as long as no 'dumb copying' took place.
I guess my involvement in the Rybka cases has led me to conclude that "dumb copying" is merely one way [and indeed, the most obvious] that copyright can be infringed. In another thread, I mentioned that one reason GCP favoured legal action by FSF/Fabien was precisely that many programmers have a "code is everything" sense of copyright [and a lawsuit would be a good way to publicise the contrary into the collective consciousness], while my opinion is now that there is much "creative expression" in the internals of a chess program beyond just the code. Chris Whittington is disputing some aspects of this.
For the specific R3/IPPOLIT comparison, I won't be able to get my R3 notes until I get back to Sydney in a week, but my recollection is that there were "too many" specific evaluation elements that would go beyond what I would expect from an "idea", at least in my book. The fact (as you've noted) that IPPOLIT's eval is almost a subset of R3 with many terms thrown out also makes a comparison difficult.
EDIT: When I spoke with GCP yesterday, he seemed to opine that IPPOLIT/R3 was "clearly" from reverse-engineering, that there was likely a copyright question to be considered [he can say more about his opinion there -- I don't want to misrepresent his position], and that there seemed to be great care that no "code"
strictu sensu was copied.