Actually, Warner Bros is one of the better supporters of the R3 DVD market. Except of course for language and subtitle tracks, their R3s are nearly identical to their R1s. The trouble with the titles you mentioned doesn't stem from their being from Warner's, but from the fact that they are some of the earliest DVDs ever released. Dual layer DVDs weren't even being produced then (which is why Amadeus is a flipper). Actually, I'm surprised that you think that the L.A. Confidential DVD was bad, as at the time of its release, it was praised as one of the better DVDs that came out. Where WB DVDs really suck though is the godawful snapper case packaging.
Anyway, I don't think it'd do much good to call up WHV to complain about the DVDs you already have. It would help though if you do call to pester them to release more Special Editions and more DVDs from New Line.
Now, the suckiest of all studios with regards to R3 DVDs has got to be 20th Century Fox. Followed closely by Dreamworks and Miramax. Yeah, there are some Fox/Dreamworks/Miramax movies on R3 out there, but if you look closely you'll discover that these particular films were all co-produced with other studios.