Talyn, please don't be insulted, but you're speaking with a lot ignorance. The reason for a plugin system is that the N64 emu authors didn't think that they should have to write for ALL screen drawing types. This is because the N64 being a Cartridge based system could have its extensibility increased with onboard RAM, maths co processors and other such extensions to its feature set. Therefore plugins could be written that could take into account such extensions and emulate them too.
Your opinion, while valid (as is everyones), is based on a fundemental misunderstanding of emulation in general. The PSE-Pro plugins (such as those that epsxe uses) were developed to offer further extension towards modern screen drawing functions, such as filtered textures and 32bit display. They, in no way, have lessened the emulators compatibility at all. Infact, those games that don't work with certain display plugins fail to do so due to custom screen drawing and/or custom texture management.
Either way, the choice of plugin implementation was decided by the devs. Ignorant "users" really don't get a look in. I'm sorry you feel that emulation should be plug and play. It isn't. The more complex the host system, the more complicated its emulation will be.
Maybe your time could be better spent researching your plugins and updating them rather then complaining that you'll have some work to do to play DC games on your system.
Cheers,
mezkal