squall_leonhart, whoa
you've said several things completely wrong
most games *are* 320x240, but not all.
the n64 can switch resolution any time it likes, up to about 640x480 - though because of memory limitations few games ran in the max res.
TVs have no native resolution, they have a native number of lines (normally 480 or 576 visible for PAL, and fixed signal timing) but the horizontal res is mainly a question of quality as to how many pixels it can differentiate.
the n64 can also choose what filtering method to apply to any texture.
the filtering in the plugin is determined by the renderer portion, seperate issue from HLE/LLE, which this refers to the microcode emulation. so you can have HLE with a software renderer (we do in 1.7, incomplete) or LLE with hardware renderer (we also do in 1.7) but both have different issues.
yes running in 320x240 will generally be closest to real N64, but it won't help when there are issues with the HLE, and generally looks bad at that low res anyway (like an N64). i recommend 640x480 with FSAA. anytime you run a low res, FSAA helps lots.
320x240 is also not a good idea because you'll often *lose* detail, many games went high than this res.