The only things that currently aren't rendered at full resolution are textures. Antialiasing (MSAA, ie the good kind) is already supported with Glide64Mk2 (also Rice, I think), and the 3D models are rendered at full resolution. (That's what setting the rendering resolution does).
If you're after pixely, rather than blurry textures (which, by the way, is NOT faithful emulation, as the N64 did interpolation on the console) the setting in Glide64Mk2 is "filtering = 2". For Rice, it's "Mipmapping = 0". However, doing this causes some problems.
Here's an imgur album with and without blocky textures. Both screenshots are rendered at 1280x960 with 16xMSAA, and if you look at the 3D models you will be able to see that they are being rendered at full resolution, not TV resolution.
You'll note that disabling the intended texture blurring causes problems with the landscape. This is because the developers made it gradually shift in color by appying a transparent, extremely low-resolution coloring texture, which is now blocky and easily visible.
There is no easily-handled distinction between UI textures and background textures, since games handle 2D rendering in a variety of ways.
Without providing some way to obtain higher resolution textures there's not much of a way to improve the quality you see here. HQ4x and the like only work well with high-contrast textures with lots of distinct edges, which doesn't apply to most N64 games. The rough equivalent for photographic-style textures with lots of detail is to go with various types of interpolation, like bilinear or bicubic, which Glide64mk2 already does. Bad news: that's what's making things blurry.
Hope that helps.