Now that it's a consuming battle, let's look at what each party has going for them:
Point 1: Kirby's digestive system is capable of almost instantaneously digesting his enemies, giving him a great advantage over Alex, who requires a ten-second cutscene for everyone he consumes.
Alex: 0, Kirby: 1
Point 2: Alex simply has to stick his arm inside his opponent to consume him, whereas Kirby must swallow his enemies whole before digesting them. This grants Alex greater mobility and convenience when the two are attempting to consume each other.
Alex: 1, Kirby: 1[
Point 3: Aside from the consuming thing, Alex has in his arsenal a variety of claws and naughty tentacles that can tear his foes to shreds, whereas Kirby is just a pink ball of fluff. While a Kirby punch does indeed hurt, it pales in comparison to Mercer's weaponry.
Alex: 2, Kirby: 1
Finally, Point 4: Kirby acquires the abilities of everyone he consumes, granting him a wide array of abilities to use in combat, from freezing to rocking out. Alex Mercer's abilities are primarily used for disguise and acquiring knowledge, and don't boost his combat abilities as significantly.
Alex: 2, Kirby: 2
The two are evenly matched overall, so the fight will ultimately rest on the environment in which they battle. In an urban city like New York, the streets are occupied by normal human beings, and therefore Kirby can't acquire many abilities from digesting the passerby. However, Alex, who can disguise himself as one of the civilians, can use the crowded streets for a strategic advantage. Additionally, skyscrapers line the sky which Alex can easily climb while Kirby has to slowly float in the air. Finally, there are many soldiers, police officers, and gangsters that will drop guns. Kirby, who lacks opposable thumbs (or any fingers, for that matter) cannot operate this kind of weaponry (even swords are a mystery), but Alex Mercer has proven to be readily efficient with guns, and even moreso should he consume one of the aforementioned soldiers, police officers, or gangsters. And if he does so, he can even send other soldiers, police officers, or gangsters to attack Kirby using his disguise abilities. Kirby is at a total disadvantage in this environment. Alex wins.
Next, we head to Dreamland, home to a large variety of colorful and unique creatures. The place is covered with wide open spaces, heavily stinting Alex's previous mobility, which relied on wall-climbing. Kirby's floating abilities are unaffected, and perhaps even aided by the lack of obstacles in the air. Furthermore, with so many creatures that wield swords or spit fireballs, Kirby can easily switch between abilities, granting him an entire arsenal of weapons to use. Alex, without his guns and tanks, must rely on only his claws to fend for himself. His powers of deception might still be in use though, depending on whether or not he's capable of assimilating strange puffball creatures. Spitting fireballs, though, is completely out of the question. In Dreamland, Kirby can even call upon the use of his Warp Star, allowing him to essentially fight piloting an aircraft. Mercer has no chance. Kirby wins.