Streets of Rage 3

"I guess the most difficult part for us is after the samurai level it seems to get crazy with how many enemies come out and how fast they are."

The ninjas that appear in the train section before the Yamato fight as well as later on are probably the most irritating enemies in the game. They're fast, their low kicks seem to make them invulnerable, and they love to jump around constantly. Make sure you take the right wall secret passage or upper secret passage in the first part of Stage 5, those 1ups really help.

As far as the good ending's final boss (Robot Y) goes, do what Lutepin said: jump kick him repeatedly. Even on the highest difficulty, most characters are strong enough that he'll die before the timer runs out. The timing isn't that difficult either, basically kick him offscreen and he'll always leap forward when he recovers (preferably into another jump kick). If you're having trouble with the timing, check Youtube, there's plenty of videos of people jump kicking him (it's the best method in both Bare Knuckle III and SoR3).

The only difficulty is if none of you are playing as Axel, Blaze or Skate. Zan's jump attack sucks horribly, and only does enough damage if you hit when he's spinning, not during the tackle portion. I think his blitzes work much better from what I've heard, but I suck as Zan.

Roo's standing jump attack is almost impossible to hit with because he retracts his tail so fast, so that's out of the question. His jump kick also sucks because it's too weak to kill Robot Y in time on the hardest difficulty, even if you land every single jump kick perfectly from the moment the fight starts. If you're playing as solo Roo, the only way I know of to kill him is to spam his back attack at the sweet spot where you can keep them infinitely stunned (aim for the closest leg's knee). Robot Y loves to jump around crazily though, so the hardest part is actually hitting him in the first place, but once you do it actually goes faster than jump kicking him as Blaze would.

Beat the final boss in time on hard setting as Zan last night. Jab-trapping can work but success is fickle. Knocked the robot offscreen and kept doing neutral-jump attacks which any character can do in theory but would depend on damage; beat the robot with 7 seconds to spare. Didn't think to try backhanders but suspect they won't be any better than jabbing.
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GT: Look up and to the left a little.