Just wanted to throw my two cents in on different ways the 'Mega Form' could be incorporated!
1. - Probably the most likely of all the options, Lucario goes Mega for the duration of his final smash (which should be changed or buffed imo) and returns to his normal form once finished.
2. - An Alt costume, something I consider highly unlikely giving Sakurai's reluctance to add any aesthetic changes to characters alt costumes but considering we still don't know exactly what the new customizable features will be I figured I'd throw it in here.
3. - Playing off Lucario's aura mechanic, when he reaches his aura limit (can't recall the exact damage figure) he turns into his mega form, either just for appearance or if Sakurai would want to follow the games all of Lucario's physical attacks would do more damage. The problem here is if this were the method for Lucario to go 'Mega' it would require Mewtwo (hopefully both make the cut) to have a similar 'aura' feature, which is something I think both Sakurai and fans would feel a bit cheated by and would ruin a unique feature.
4. - If Sakurai were to follow the games, both Lucario and Mewtwo would have to just be known as Mega Lucario and Mega Mewtwo, only acting as there normal forms when they enter the stage, something I think would go a number of ways, fans would either be happy to just as the mega forms, fans would prefer playing the normal forms and some fans would prefer it if it was a genuine gameplay feature, again I don't see this being a likely option.
5. - If you look at the recent Pokemon movie, Mewtwo has the ability to transfer in and out of his Mega form at will, if this were to be incorporated both Lucario and Mewtwo would sacrifice a special move in order to transform just in a similar way to Zelda/Sheik. Again, for balance issues, they would have to be thought of us two separate characters (for example, Lucarios physical attacks get stronger but due to increased weight he's slower and has a lower jump?). Again, I think it takes away from Zelda/Sheiks unique function and the fact they can be thought of as two separate characters makes it far more compelling than just going between 'Mega' and 'Normal' forms.
6. Sakurai decided that just because both have Mega forms doesn't mean they both have to enter them in similar fashions, so Mewtwo could go in and out of his form with a special move and Lucario would only transform when he hits his 'aura limit', this would probably be my preferred option as it gives both characters an element of originality while essentially being the same thing, however since it goes against how the actual forms work in Pokemon I dont know if Sakurai would consider this.
Sorry for the long post, just had these thoughts and had to put them down somewhere! This is all assumed both Mewtwo and Lucario make the roster cut, which I believe both should. In all honesty, I doubt the forms will be used at all and even if they are it will simply be when both characters use their final smash and both returning to normal form, while I would much prefer it to be a gameplay mechanic, I think that's the only option we'll probably get!