1. Nope, but this really has nothing to do with how popular he is, just that the devs put a statue of the first Mega you get in the tower that you'll never go into again.
It doesent matter if you go into there again or not its there and hes the only with it.
2. Yes, actually, and that's all of them. Lucario is just the setpiece used to represent Mega Evolution for that short time in the story, then never again. The real star is Mega Evolution itself, which is relevant far longer than Lucario within the story. Again, this has no bearing on his popular reception or how recognizable he is, so it's another null point.
Not exactly mega evos wouldnt exist with out lucario since he is the reason they were discovered in the first place so as long as Mega evos stay relevant so does lucario Like I said it the cannon part of mega evo's revovle around him.
3. Yeah, Gardevoir and Gyarados. They have all the plot related to them that Mega Lucario does.
Valid point.
4. You still keep referring to in-game points. The game itself has nothing to do with how popular or well-received Mega Lucario was. It was just who they chose to be the first one, likely because it was one that they could safely give away without it being too consequential to the story; Lucarios are insanely easy to get ingame, so they figured giving you another wouldn't hurt, unlike something like Gengar or Houndoom, who you actually have to work pretty far in to get.
How hard or how easy it is to catch him is irrelevant and I dont think there is a excuse as to why they made him important like that honestly I can care less why all I know is that they did it thats all that matters is that it happened, and if your sick of ingame importance why not check out the tv show lucario is on "Pokemon sunday" been there since gen 4 started.