First of all, let me express my pleasure at being able to converse with you, Christopher!
Star Trek (2009) has a 94% approval rating on Rotten Tomatoes, an 8.2/10 rating on IMDb, and a 4.3/5 rating on Netflix. For comparison, TWOK has 90% on RT, a 7.8/10 on IMDb, and a 3.7/5 on Netflix. ST'09 is slightly more popular with audiences and critics than TWOK, and has received widespread acclaim for its drama, characterization, and storytelling.
Well, sure - ST09 has cooler special effects! Of course it has better ratings!

(point taken, though - I love TWOK more than ST09, clearly - but is it nostalgia coloring my preference? I think that's a discussion worth having!)
Plus, TWOK never had anything as testing of an audience's suspension of disbelief as Kirk just happening upon Spock Prime in an ice cave.
Oh, come on. A cadet simulation rigged with live explosives?
...
dozens of great examples of really solid inconsistencies...
TWOK is nothing
but plot holes that stretch suspension of disbelief to the limit.
Yes! Agreed. However, since they are surrounded by otherwise compelling film making - these nit-picks don't really take away from the experience as they did for me in ST09. Speaking for myself, for ST09 I didn't feel there was any "there" there... I mean nothing compelling enough to not make the convenient stuff too noticeable. For me the ice-cave meeting was so 'convenient' that it actually shocked me out of the 'world' of the film, unlike, say, realizing that Chekov never met Khan [though honestly at the time I first saw TWOK I wouldn't have realized this] -- and this coincidental meeting is not just violating "Trek canon" or "inner consistency" within the world of Trek, something like many of the flubs you mentioned from TWOK were doing, but its actually just lazy storytelling in my opinion -- though I do appreciate the interpretation offered by Therin - that they're destined to find each other -- but still at the time I felt let down. Thankfully I had read the Countdown comic! Otherwise I think I'd have been even more baffled.
As to the charge of "nostalgia" coloring such an interpretation as mine, I have to say -- possibly, but probably not in my case. I mean, for me, a guy who read trekmovie.com every day for a year and a half before this movie came out, so excited to see the updated new cast, so ready to have the adventures of Kirk and Spock handed to a new cast and crew, really WANTING this movie to be great (as opposed to much of the pre-hate I read all along) it still managed to leave me feeling thrilled but ultimately empty of the things even the worst "exact replica of the US on another planet" episodes of the original show always had -- heart, intelligence, and a serious interest in sci-fi ideas and their ramifications.
ST'09 is a continuation of a pattern that TWOK originated:
Star Trek films as visceral experiences where logic and plausibility take a back seat to emotion and energy. Neither one has a plot that really holds up to careful analysis, but both get their popularity from their emotional cores, from the characters and their interactions and the way they make the audience feel while watching, even if those feelings give way to
Fridge Logic criticisms later on.
For me TWOK is made ultimately great by one synergistic thing -- the Genesis device. The new film has nothing to play with like the idea of remaking entire planets, even if its ultimately a Macguffin to get to the Kahn-fight, the way you can roll it over in your mind, play out its consequences along with Kirk McCoy and Spock for the universe -- this is what makes Star Trek what it is for me -- and while the new film had amazing breathtaking action in spades, it doesn't really have anything like a great sci fi idea for me. The closest it comes is the question of how much does Prime Spock tell them, but it doesn't get much screen time -- mostly dealt with in what to me seemed like a highly-over-expositional cave scene between Kirk and Spock Prime.
So which one you prefer is really a matter of taste, not of any fundamental difference in their respective quality or intelligence.
Of course! Granted and agreed, always. Its very tempting and too easy to write in objective language when having these kinds of discussions but I assure you at the bottom I know this is true for us all, and I would not want to make any claims to anything other than my opinion, however strongly I make it.
Having said that -- I could have done without the destruction of Vulcan (seemed to be an irreverent and unnecessary "this ain't your daddy's Star Trek! Nyaah!" from the new creators, but without much dramatic punch or need ultimately), so many in-joke references that were just tossed off (reminding me too much of all the TV-show film-remakes of the past couple decades....) even if they provided momentary joy, I would have preferred another entry in the series worth quoting itself.
But Christopher, tell me -- you love Star Trek, you are writing for this new universe -- do you love it? I mean, you must, but do you see the new Trek creators as having a bead on just what made the preceding entries into something we all love so much that we read (and write!) novels about them and spend all this time online, etc., etc.,? Because I wanted to so much but after seeing this film, I was left a bit hollow.
Maybe in ten years I'll love it when the nostalgia kicks in?
I can also tell you that when I watched the first episode of TNG I was hoping Picard would die so Riker would be captain! So first impressions can be suspect!