Without going point by point, I guess the "bigger picture" areas where your post just doesn't make sense to me are:
(1) I don't really consider Jason to be the bassist for the "Metallica we all grew up with." That would be Cliff. Jason was the "new guy." And while melded his playing style very well with what the band were doing, and fit well with them onstage, even he was always clear tha he was somewhat of a misfit in a sense.
Three points regarding that:
1. I'm twenty nine years old, I started listening to Metallica when I was a teenager, Jason's Metallica is indeed my main Metallica and that goes for whole lot of people of that age group.
2. You might have seen Metallica live in the 80's with Cliff and lived through the RTL and MOP release dates and consequent tours but that's somewhat of a hardcore case and rarity as -even in the older age group- it's somewhat exclusive to U.S. audience, not even casual music audiences, but the people who found Metallica without MTV or radio*. Point being regarding the 80's and Cliff Burton: With no videos, radio play or T.V attention, if you're not in California or an absolute hardcore of a metal head with metal head connections: you have no "stuck" image Metallica with Cliff Burton.
* I know there are at least 5 people of that group here including Barto, Orbert and chefkingshmegland.
3. All the official and unofficial releases that featured the band live on video came after Cliff Burton's passing, nothing but Cliff Em' All and a few more audience shot footage to make a fan -who does not fall in the category mentioned in the second point- cling on or connect to Cliff Burton's Metallica.
All that being said I have to make something clear: Cliff Burton was most definitely the most creative of all Metallica bassists and the most unique in style and technique, I'm only talking about image of Metallica which most fans connect with, saw live and familiarized with, which is Jason's one.
(2) Trujillo has always been a thrash bassist, just from a little bit of a different angle with funk and punk thrown into the stuff he did with ST back in the day. But I think even if you went back to the time when Cliff died and they were looking for a new bassist, if someone had said they were looking at Trujillo, I certainly would have felt that he would have been a logical choice back then.
Metallica auditioned Les Claypool from Primus and he was certainly a better bass player than both Newsted and Trujillo at the time but they didn't call him back, he did not fit the image and the vibe, apparently that part I would never be able to explain but they were not looking for technicality nor unique styles, they were looking for a straight forward GRRRR metal head who looked and behaved like they did, could learn and play the songs and would do as told and Newsted was that guy. Burton was had the best of both worlds and that was hard to replace, perhaps cause they didn't look long enough as they had to get back on the road.
The standards they used in the 2003 bass auditions were completely different than those of 1986 and Trujillo worked for them.
Finally let me get a little shallow here and say that how Trujillo presents himself is also a big factor in my rejection of his fitness for Metallica, the fuckin basket ball jersey and the shorts and the whole spider walk thing is just too.. something else other than Metallica, something cool and interesting that I would find appealing in a different band but not within the Metallica themes and vibe at all.