The inevitable downside to how
Deus Ex: Human Revolution - The Missing Link is handled is the already mentioned disconnection and what it means for the gameplay.
For starters, you are stripped of all of your Augmentations at the very beginning, forcing you to restart your character from scratch. Although you still remember how you decided to tackle the game, there's no actual in-game record as to how you decided to take things on. All of your decisions prior to this point are meaningless and any decisions you make during the chapter have no bearing on what happens in the main game.
Personally, I wasn't completely thrilled with the idea since I tend to build a link with characters I've spent hours with, planning and developing to fit my own personal play style. Granted, nothing stopped me from continuing that style in The Missing Link, but it lost something considering everything I did had absolutely no impact on the bigger picture.
At the same time, I can see the potential in restarting a character. It allows for a certain level of experimentation in just how drastically different one play-style is from another. I stuck to a mostly stealth build in the original game, so I ended up trying out a brute-force style this time around. It took adjustment, but I appreciate seeing the other side of the fence.
Missing Link does a great job at keeping things flexible and offering lots of opportunities for explorative play. You can tackle most situations in a number of ways, and it actually manages to make a few improvements - most notably the lack of the wedged-in boss fights that plagued Human Revolution. Instead, you get a really interesting fight built with multiple skill sets in mind. Unfortunately, the small play space makes backtracking a necessity. It offers an opportunity to snag items you may have passed before, but return trips aren't very exciting.