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I love both so it is hard to pick one over the other for me... but if I had to, I would go with Latios simply because I like the color blue a bit more than red. I also used Latios more than Latias in my games.
They always take forever to capture for me though >.>
Over the years I've learned to just love both of them. At one point I loved Latios more and at another point I loved Latias more and now they're pretty balanced. I don't remember any times I actually caught Latias, though, so most of my love for her comes from her design and the Movie, I suppose.
Latios on the other hand I actually have a soft spot for because when I first played Ruby I caught Latios with the first ball I threw - a Premier Ball. It was certainly a highlight for me when that happened.
I remember how massively excited I was to catch these two....they're adorable. Saved my Master Ball specifically for them. I chose Latias and friend chose Latios, way back then I preferred Latios a bit more but lately I love Latias so very much since she is just that innocent and precious lol. Especially in the movies. Going forward I'll probably keep choosing Latias. * *
Latios. Yes, Latias may be a cuter Pokémon and the red color really helps, but Latios looks like a more serious, powerful and generally "tough" Pokémon. I also prefer blue over red, so that's a big point.