1) Running natively is better. Better performance, better compatibility, and it doesn't have the graphical glitches that occur from the DSTwo skipping every other frame. (The DS cartridge slot can't transfer a whole 60 frames a second)
2) Even not using TempGBA, the DSTwo still has SNES emission and bagplug to make it stand out.
GBA Emulation is a feature for DSi and 3DS users who can't use a slot 2. It's not that you can't use it on a DS Lite, it's that you shouldn't want to because better options are available.