THis is a tough one but I've always believed it boils down to what you prefer. 

Crash 2 is easier but a lot of it's secrets are super obscure (like the Nitro steps) and it's just as beautiful, but more fair.

Crash 3 is the easiest, but it can kinda put you on auto-pilot, and some of the vehicle levels can get drawn-out.

However, all in all, I've gotta give it to Crash 3. I just love Crash 3's level design more. The relics are an incredible way to add longevity, the boss fights are the best they've been (Dingodile and N. Gin especially), and the idea of time travel really let them take advantage of any time period they cared to muster. And they didn't just use the idea for cliched ideas like the Egyptian Levels and medieval times. They have you going back to the 50s of America, the aerial battlefields of World War I, the Golden Age of Piracy, ARABIA, and even Atlantis (I think that's what the underwater levels were meant to be.) It's the most complete package of Crash ever, and I sincerely hope that the developers of the N. Sane trilogy put more of Crash 3's genius advancements besides the time trials in the older games.

Besides the Naughty Dog games, I'd say my favorite is Twinsanity, followed by Tag Team Racing.