The first noticable problem is that it's lacking the licensed expansions - something that to fans of these would be a huge loss of content. Once again, it's got the original three episodes and the fourth 'The Birth' episode as is standard, but that's where the similarities end. The Anniversary edition is a different story. Doing a search for videos of these episodes is probably the best way to gauge your experience - but if you love the game like I do, even the worst levels are still incredibly fun. I love Duke Caribbean, but am not a huge fan of Nuclear Winter for example. These episodes are varying in quality and are very subjective. On top of this, it has the three licensed expansions - Nuclear Winter, Duke Caribbean and Duke It Out In DC. It's got the original three episodes, plus the additional 'The Birth' episode - which is standard for Duke releases.
The Megaton edition has everything you'd expect if you were a classic duke fan. This includes, but isn't limited to 1.3d's original release, the plutonium pak, the atomic edition release, the original kill-a-ton 3-cd edition, the steam Megaton edition, the steam Kill-A-Ton edition and of course the 20th Anniversary.
I've had experience (and own) most versions of Duke.