Exactly. But let's not equate dragon with flying. It's a complete character that you have the potential to work with to solve complex puzzles requiring the skills of the pair. Working together with a character that has just as much influence as Link is very fun and adds a level of depth to the game-play that Link simply can't achieve on his own. (As we saw in ST)
Plus, if you have a dragon that grows over the course of the game, then eventually, you will get into dungeons of a massive overworld-ish scale. I would love that. And, the growth in itself provides the perfect transition. You start in a small dungeon to re-learn the basics and get your footing, and then you take off near the second half. (literally).
This entire section of the forum is speculation and ideas for the future. Anything is...well...fair game.
Besides, take a look at what a dragon could potentially bring to the series.
Steed for Flying and Gliding (No…really?)
Steed for traveling the ground, too
Breath Fire in numerous ways, such as a standard flame, whip, long-distance fireball that slowly fizzes out the farther it goes…you name it.
Other breaths, such as ice or light (think the arrows)
Tallon, Tooth, and Tail physical combat for him/herself
Aerial combat for both itself and Link
Digging (Why not?)
Gusts of wind and potential shield (via wings)
Hold down big switches (Ok, so it’s not the most impressive trait, but I’ll bet you will use it)
Take down big obstacles that bombs just can’t handle
Climb up certain wall surfaces
Work in one area of a dungeon while Link is in another (This is a big one)
Be a huge plot point
I’m sure you can think up many more as well.
So to sum it up, a dragon is a powerful Steed, Fighter, and Ally, and introduces a montage of puzzle/dungeon mechanics- much more than pure flight would, at least.
And while I'm at it, why might Link decide to team up with a dragon? Maybe that dragon holds the spirit of Din inside him/herself (check the pic, specifically at the tail), and there are actually two others representing the other goddesses. Link might have paired up with the one of Courage, but that dragon was captured/killed, the villain thinking Link would use that one in some sort of prophecy. So, Link pairs up with a much bolder companion.
That’s one theory. Let’s see what else we can come up with, shall we?