I don't know about Deus Ex - I played the original when it was released and it was phenomenal, but the sequel was a serious step backwards. I did like it, but it was pretty linear and was missing a lot of the customization the original had.
Human Revolution I thought was a great addition to the series, but it still doesn't capture the magic or open-ended gameplay the original had. It's a great effort and far better than the second game, but there's still room for improvement. Just my two cents though.
As far as what I think gets better?
Diablo and Metal Gear. Probably both been mentioned but I'm lazy and can't backread

Diablo 1 was great - Diablo 2 improved on the original in many ways (personally I wasn't a big fan because I felt a little let down after a 5 year wait, but it is technically a better game), and Diablo 3 has really taken it to the next level now that it's been improved due to user feedback and tweaks.
Metal Gear, regardless of what you think of the storyline, has improved leagues over each iteration. Each game has better gameplay than the last, and isn't that what this is all about?
Now if you wanna talk about series that have regressed, just look at Dead Space for a good example. Each game got worse and what started as a survival horror turned into a 3rd person action romp. Mass Effect pretty much pulled the same trick.
