The guidebook gives information on how Phoenix had to be defeated: "Its body was wreathed in flame. You defeated it by plunging it into a lake". This indicates that Wander was not able to climb its body straight away. In all released screenshots of Phoenix, Wander is seen riding Agro, so it can be assumed she was vital to this battle.
According to an old Team Ico Gamers Blog post, Phoenix was removed for being overpowered and also because it required a huge arena due to its attacks.  (This would later be confirmed by an interview with Fumito Ueda conducted by French gaming magazine Chronic'art.)
There are two proposed locations for this colossus' original location; the first at D3 on the map, where the same trees seen in several of the beta screenshots can still be found in the released version of the game. The second is at quadrant I4; where matching texture and data evidence also suggests the colossus once dwelled.