I liked this essay on plot holes (and more generally good writing) despite the all caps and rather long winded style:
http://birthmoviesdeath.com/2012/10/30/film-crit-hulk-smash-...Personally, I found the strength of TBP and DF to be the depth that Liu achieves with his plots at the highest level, and it's important to take a step back and not judge him as pure hard SF (as it seems to have been sold to you, based on your review) but as a writer of literature using SF as his medium (as might have Heinlein, PKD, or Asimov who is his clear and direct inspiration).
The science "plot holes", the suspension of disbelief were I think fair play as a base to deploy his explanation of the Fermi paradox (which is to an extent the point of the whole series). Like psychohistory in Asimov's Foundation or Batman's seeming invincibility in Nolan and Ledger's masterpiece, it helps plot development and the greater ideas about human nature, politics, information operations and so on that are put forward by the book.
The analyses of human nature, particularly of bureaucracies and destruction via inaction (to quote Admiral Rickover, "the person who disclaims responsibility is correct: by taking this way out he is truly not responsible; he is irresponsible").
What makes a good book/movie/narrative work of art? To me it is increasingly about the plot and, to quote FCH, about how long the work can make you think about it after you're done reading it. It's clearly working since it's been weeks since I've read the books and I still couldn't resist making the quip despite the increasing amount of karma it is costing me for being off-topic.
Compared to another famous recent Hugo winner, Rainbows End, I thought Liu's work was much more enjoyable, because it was technically unpolished but had a great, interesting, innovative plot (and I'm sure half of the polish went missing in translation), whilst the latter was technically impeccable if now a little dated, but had little in the way of plot; the plot was almost a frame in which Vinge was developing his ideas about wearable tech and information operations' logical conclusion. It's like Esterhase mysteriously putting on a bad Hungarian accent in Smiley's People when he was the epitome of the try-too-hard British arriviste in TTSP - you can forgive them the glitch since the core of the writing is so exceptional and both Esterhases were fabulous characters with great depth.
Liu's ability to toy with the reader and take unconventional paths is rather rare in today's crop of writers. I would draw a parallel there with many of Charlie Stross' books; the polish is not always there, but he keeps reinventing himself and (at least for me) each foray into a new genre or avenue of thought is a success (and a source of great movies and books to explore).
As a side note, I thought it was one of the few successful depictions of a truly alien culture (what you call near-Strong-AI?) in SF today (and no, I didn't think Vinge's FOTD's Hugo winning hive-dogs were truly alien: put human heads instead, set it in medieval "Ireland-Spain", and you get Game of Thrones, down to an epic fire battle before the walls of King's Landing).
As a second side note, isn't it fun to draw parallels between TBP and the real world? How do you, today, as the PLA, deal with the fact the NSA can hear and read everything except your thoughts when planning defense strategy? Suddenly the sophons don't seem so alien... I don't like tin foil hats, so I didn't try too hard to put myself in the Chinese position, but it was definitely an interesting line of thought.