I can't say as much for the Marth MU with Roy, but from what I've played with Roy I just feel like he's at a disadvantage. To me, for some reason he feels so damn heavy and I'll be watching for a Back-roomer/Mod to come in and tell me his falling speed matches Roy, but I kid you not when I get knocked off I feel like Roy falls like a brick even with proper DI.
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Back to the Marth MU discussion, sorry I got side-tracked. Playing Roy against Marth is just tricky because you really need to get your combos out, and since most Roys/Marths don't use counter, because of how badly you'll be punished if you mistime, you're free to try to hit those combos out as soon as you get the chance. Just don't forget to toss in a throw or two, remember his throw isn't very powerful, but it's really meant to have combos mix right into it after the throw. I'm not saying go bat-**** crazy with your combos, but with Roy I highly recommend being more aggressive, the only catch is you should REALLY know your spacing. But, in general if the Marth is about your level on terms of skill, you should expect to lose the match, Marth's attacks just come out faster, and to top it all off his recovery is just better. And in my opinion Marth can just chase much better off the ledge, because even if he misses he can still beat you to the ledge, and wait for you to make a grab for it.
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Also, someone tell me I'm crazy but did Roy's in-air vulnerable frames get increased (when he's hit into the air)? When I'm hit into the air, I literally feel like it takes two-seconds (slow seconds by the way) just to even respond at all, when with any other character, even characters like Ganondork, I have literally what feels like less than a second to respond, in any way.