The final version of MKT for PSX and PC has gameplay identical to UMK3 but with characters, and moves added on. For instance, Sindel has a double fireball, but other than that, she plays basically the same in both of them.

Scorpion changed more dramatically since he gains a forward teleport that really adds a few options to him.

Kung Lao is limited to 1 spin per combo now, but he can move while spinning, which breaks it in a different way.

There are a ton of such additions/changes.

The new content added in Trilogy tends to be broken.

MKT for N64 is a different story. It's like an incredibly broken UMK3 with broken content added on top of it. A lot of people know my favorite example of its brokeness so I won't beat that particular horse. It's a mess.

MKT and PV versions are very similar to SeGA Saturn and N64(really they're both broken,tough it's harder to make infinite combos on psx,i don't know why).
MKtrilogy have just longer loading times and a less smooth graphic than UMK3 arcade version.

The Saturn version of UMK3 is broken in it's own way. MKT for PSX/PC got the UMK3 content correct, Saturn UMK3 didn't, which is why you can combo after aaHKs in the corner and why there are tons of weird rules that make the game more broken.