From about 1/3 of the way in, 009 Re:Cyborg steadily goes from passable to bad to worse to horrible, eventually coming to rest at "WTF?".
The last anime I can think of to spend such massive resources so ineffectively from a dramatic standpoint was "Metropolis" (2001). And that was a considerably better film.
Indeed 009 Re:Cyborg is as close to "cost no object" animation as there is these days. The military hardware is all rendered with fetishist detail, the backgrounds are sumptuously drawn, and all manner of computer- assisted effects enlisted.
The main problem with this film isn't even the overwrought and meaningless plot. I'll buy a lot of things, and though a 9/11-inspired story about pseudo-religious communion with "voices" that induce terrorist acts isn't really my bag, I'd be prepared to let that just drive the movie along and join the ride.
I should add I have no emotional investment in the original series, so they can preserve or desecrate the memory of the Cyborg: 009 TV show all they want. As an aside though I note uncanny resemblances of two characters in particular to Tony Stark and Eric Banner will probably seem odd to Western audiences.
No, the main problem with this film is that its empty of any genuine emotional content or character interaction. Stuff happens. Characters stand around staring vacantly, stating in the declarative what needs to be stated to convey information to the audience. To break the monotony there are frequent bouts of wordy philosophical ennui. Then there's a gunfight or some random and frequently ludicrous action sequence. Rinse and repeat.
And the ending has to rank up there as one of the weakest and laziest bit of scripting in the history of anime.