The question isn't will we be able to see the red Gyarados, it's more or less will we have the chance to battle and/or catch it. Red Gyarados is an important part of the main story, but that doesn't mean we'll have the chance to catch it. The rumor going around is that Lance will possibly capture the Gyarados rather than the main player, and may or may not fight you with it in the Champion match. (Which is quite doubtful considering it only resembles a dragon and is not actually dragon) But this could possibly implimented so that everyone won't get a shiny really easily.
Personally, I hope they'll offer it up to catch it. I loved the red Gyarados in G/S/C and it became a deep part of my main team. It was really a treat as the first shiny I caught and most other people probably caught. It was just such a unique concept and it really delved you into how twisted the members of team rocket were.
And yeah, the value of Gyarados would drop because of the amount of them offered up everywhere. But honestly, it would give the games so much more nostalgia value (bringing in many old players, along with letting the new generation of fans to see such a cool thing involved with the story) and really the Gyarados is a very important part of the story. So I say if they're gonna have the Gyarados at all, let it be red, let it be catchable, and let the player be the one to have the chance to catch it.