I think for now, Moves should be eased into in the games in general. Abilities should strictly be reserved for the third GCeA, which JD did say was basically us using our best Pokemon from both the previous games (I think. He probably forgot it, too.)
On another note, I just love the drama in Silver-though there is one problem with it. Specifically, that Seth's Ledian died...Wasn't Seth's Ledian the one that was Shadowed and stolen from him earlier?
...Yhea...You kind of get the issue, now. Seth's Ledian can't have died and been Shadowed and Stolen unless Seth's Ledian was killed directly by Dredd while it was Shadowed and separated, which clearly didn't happen. Unless you're making that a direct result of Dredd's illusions, that's quite the plot hole.