It also lacks the low resolution look of the PSX/N64 versions. Only time will tell though.
Things exclusive to the console versions, which should not be on the arcade:
Raiden spelt with a Y. Selectable Shao Kahn/Motaro/Kintaro/Goro (not selectable on the N64, except for the MK3 bosses via a cheat code). A non-solid-black Noob Saibot (e.g. a dark version of Human Smoke). No usage of the standard Midway/Wiliams test font in the 1P/2P/8P menu like the PSX version uses. A semi-transparent life bar (arcade is dithered red/transparent pixels when you get hit).
If someone can hack the shitty Genesis version of UMK3 into 'Ultimate Mortal Kombat Trilogy', why can't they do the same on the arcade? It's a perfect candidate for MiSFiTMAME.