This reg does look better and will handle a higher amp draw, but those caps look huge. I don't know how you would fit that in to anything without relocating the caps or swapping them.
Additionally, any voltage regulator will put out heat. That's just inherent, and isn't something to necessarily be afraid of. These are switching regs, which have high efficiency (90%+) vs. a linear reg, like the 5v reg on the n64 itself. Linear regs also put out far more heat.
The 3.3v line draws about 1 amp, which is enough to squeeze heat out of any regulator, be it the pth08080, the 5v 7805 on the board, or any switching reg mentioned here thus far. I would try to find the regulator n64gcmod suggested but in a package with smaller caps. The efficiency is better than the one I listed.