Different strokes and all that but I like Prey a lot more. I thought MD was a massive disappointment and only clocked 20 hours. Gameplay was a step up from HR but the Story and characters were a massive letdown for me and that's pretty key in a Deus Ex game. It was a solid (read: 'meh') game in its own right but a far cry from what I expect from a DE game.
I liked the story for what it was - a very low key thing, simply an investigation of a terrorist attack and not much more. But the sidequests were where the game shined and those were pretty excellent.
I liked the game play in Deus Ex: MD, was not a fan of the locale due to it not matching deus ex, but gameplay was damn fun. Problem was the story telling did not live up to my expectation which ruined the experience a bit.
I loved Prague. Not just because I am from Czechland and visually they quite nailed it (even if they butchered the language), but it was the densest most detailed city hub in a Deus Ex game to date, very atmospheric. Especially at night it reminded me of Vampire Bloodlines quite a bit (in fact the game as a whole is more related to VTMB than to Deus Ex 1).