They're a completely random list...most of them aren't even comparable. Deoxys vs. Rayquaza would be a better comparison due to the BSTs. You've also excluded many other event pokémon such as Deoxys, Manaphy (and Phione), Keldeo, Genesect.
Although with regards to Mew vs. Mewtwo...hard to decide really. Mew's fairly powerful in-game, extremely versatile (learns every tm and move tutor move possible :P - makes it the world's best HM slave. I have two so that's potentially all my HMs covered in a game). Mewtwo is offensively an absolute beast. However something about the Kanto legendaries...when you meet them it doesn't seem much of an exciting event compared to say Rayquaza in Emerald, Dialga in Diamond, even Ho-oh in G/HG (although that has very little backstory). For that reason Mew wins it for me due to its rarity, it feels much more special just seeing it in my box, and when it pops out of its pokéball when I trade it over from another game.