Can't argue with much of what you said (nor do I want to), but a few thoughts:
1. I wouldn't worry too much about ISG and its report, both have been (rightly) discredited even before they were finished. Sure, they'are and will be used by Dems and other usual suspects, but that's why these commissions exist in DC - to be used, and if not this commission, then something more credible and more difficult to disregard would have been used, so this ISG may be a blessing in disguise. ISG was praised by Iran, Syria, "Palestinian" leaders, Jimmy Carter and criticized by Israel, Iraqi government and even more sane Democrats - so it's at best a double-edged sword and could be a downright poison pill for Dems on The Hill.
2. Like Rummy implied, with the new Congress, SecDef's job has changed from actually running the DoD to spending most of the time liaising with Congress, i.e. his job is being a "diplomat" which Gates can do credibly given the right instructions. He's not that much of Bush-41 "inside man" as Baker-Scowcroft-Powell et al gang.
3. It's not very easy to explain even with good communications skills (even to some on FR) that Crips-Bloods ...er, make it Sunni-Shia 13 centuries-old internecine warfare and settling of old scores and fight for power in Iraq doesn't at all mean that "we are losing war in Iraq" and may actually be helpful to our long-term goals and our immediate efforts in fighting al-Qaeda and other Islamo-nazis in GWOT. That's supposed to be understood, at least by conservatives, and Bush tried to make that point implicitly in a few speeches before elections, and it should've been driven home by election machinery.
4. As far as elections, he couldn't be that effective when Congress-critters ran away from him and policies and played to al-Media. Also, many lost because Dems provided "faux conservatives" with money and conservative scripts, and GOP election committees haven't reacted at all - not with money, not with the message, not with strong GOTV effort beyond simply repeating phone banks' calls to landlines which are at best ignored and at worst are annoying. Not on national nor local level.
I would put 90% of the blame on elections results on lame performance of GOP Congress itself during the year, caring more about scoring points with al-Media against the President and also almost no efforts in pointing out the obstractionist Dems (difficult when they had made little effort to pass anything except pork bills). Pork never works for Republican base, only for Democrat base and many independents - GOP played the Dems' game on Dems' field. Many in the conservative base stayed home on election day. Even with all that many Dems wins were razor-thin, and they won thanks to old Clinton machine tactics of pretending to be "conservative" or at least not San-Francisco liberals in values and ideology.
5. Ideology is important, communicating ideology and policies stemming from it clearly and effectively is equally as important.
Paraphrasing Einstein's "Science without religion is lame, religion without science is blind", "Ideology without communication is lame, communication without ideology is glib".
Lack of communication skills and efforts are my biggest disappointment in President and most of his Cabinet and his PR apparatus (remember Scott McLellan?).