No problem with the RTP at all. Where I think a lot of the hate comes from is that so many people use it to make a completely default game (and not a good one, at that), and then the RTP becomes associated with bad games. A lot of games over the years have come out using default graphics, scripts, and audio, but also default sample maps (no attempts at editing them) and the default database (using Ralph or Eric as the main heroes), including all default items, stats, etc.
Using stock resources is one thing, but building a game requires design choices. I do find a bit of fault with some of the audio in Ace and most of it in VX. But audio is the one thing that can be changed with almost no effort. Heck, the ReStaff submissions alone has enough audio to replace the RTP several times over, and they sound so much better.
What you do with the resources, well, that's part of the trick. Indrah's tutorial on edits, recolors, and clumping can really give you an idea of how great the RTP is, and how much it can be improved upon with hardly any experience at all. Scripts can add atmosphere as well, as others have pointed out with parallax mapping and light effects. But even the event commands can garner nice results. Tinting maps, adjusting the pitch of audio, creating weather effects or animation in the course of a cut scene...