Usually, buttons in parentheses are buttons you hold down; for example, "(BL) up, up" would mean that you keep block held while performing the "up, up" part.
The easiest way for me to beat Motaro in UMK3 and Trilogy is to take heavy advantage of the added feature of being able to start combos in mid-air (something that wasn't in the original MK3). Basically, you just leap into the air, perform a punch or kick while on the way down (you can only use a kick when jumping straight up) and start right into your combo. To go a bit more in-depth, here's a description of what I do:
As Scorpion or Human Smoke (the characters I play as the most), I'll often wait until Motaro is near me, jump straight up in the air, and then on my way down press HP (the mid-air combo starter), HP, HP, HK, back+HK. You have to make sure that you keep the combo tempo starting with that initial jumping punch, because if you do it correctly it turns into a normal combo. He'll often block at least a couple hits, but if you keep this up you'll be home free.
Another thing to take advantage of in Trilogy is that Scorpion and Smoke's harpoons will connect with Motaro (which didn't occur in previous versions of the game), so use that at will. Some other projectiles wil also hit him if you're close enough, actually, but the harpoons will work from anywhere. Also, if Motaro jumps at you, try to hit him with a jump kick and immediately run in and perform your combo as he's getting back up.
Basically, I think a good rule against Motaro is to stay in the air as much as possible. This won't always work to your advantage, but it gives you more opportunities to catch him without him catching you.