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Dialga comes from dial, a reference to the first episode of the johto anime "Don't Touch That Dial!" foreshadowing with its power over time that we would be going back to the past as seen with HGSS. The ga comes from gahhhhhhhh, a screaming noise such as the one made during its signature move roar of time.
Palkia is a combination of P, hall, and kia. Palkia is the deity of space, and hallways connect far apart spaces. P replaces the first letter due to phospholipid heads being standardly represented as spheres, much like the gems in its body. Similar to hall, kia is included as it is a car company and cars are used to travel between very far apart spaces. Kia was chosen specifically as it is a korean car company, and as Gamefreak favored Dialga over Palkia (note Palkia is weak to Dialga's signature move while Dialga takes neutral damage from Palkia's), they gave it the fitting name of a company they didn't like, due to the long standing rivalry between the two east asian nations.
