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Because it's plain and functional looking but also a little quirky, is fairly good in-game and used to be good in the meta without being overpowered, a nice stat-balance that pairs well with STAB-Earthquakes- my favorite attack- and with its typing, movesets, and ability to fly, it makes it a dynamic combatant to plug into fanfic battles. This was not a Pokemon that I loved at first sight, and didn't catch one until my second playthrough of Ruby, but it grew on me to the point I started using her as team leaders each generation (always females, which bothered me because girls couldn't pass down that precious Earthquake TM). Now I have 7 lvl 100s and use them in every casual competition I can.
I've got mixed feelings about no-mega. On the one hand, a mega might make it relevant to the meta again, but on the other, I've despised the design of almost all the mega forms and feel they could only ruin Flygon's top-tier aesthetics.