In the first movie, Evelyn is a geeky, clumsy and shy librarian, whereas by the time of the second movie, she has become a confident warrior and a master of swords and guns. While some may find this a jarring change, if we consider what she's been through, along with her choice of husband and lifestyle, it's a very believable change for the 10 year gap between movies.
One of the deleted scenes in the first movie involves a pair of zombie priests digging out the Book of Amon-Ra before Rick and Johnathan can get to it, wherein they're sprayed with the same acid that killed the group who unearthed the Book of the Dead. Why delete the scene? Because no doubt the Egyptians would not have wanted to make it as hard to kill the creature as it would have been to release him.
Although the director did say that he cut that scene for pacing purposes.
What exactly were those pillars Alex knocked over in the sequel holding up?
In the first movie, Pharaoh Seti's "crown jewel" city was Thebes. However, in the prequel part of the second movie which took place a thousand years earlier, The Scorpion King (or his look-a-like grandson), destroyed Thebes using the Army of Anubis. Then, when Rick and Evie are at Thebes, the same fallen pillars are on the ground, unmoved for 5,000 years. Shouldn't have Seti have had the place cleaned up, since it was his capital city?