The first game is definitely the best, it's a fucking masterpiece. It has its flaws, but they don't take away from the experience or ruin the gameplay or atmosphere.
Invisible War is unplayable garbage. Everything about this game just sucks. Shitty engine (when I used to play it, I noticed that this game runs THREE different .exe files before the game starts), shitty graphics, shitty maps, shitty dialogue... They even fucked up the inventory system. The first game had goofy ass voice acting yet it fits like a glove whereas IW has monotonous extremely boring voice acting and the plot is basically the same. I felt immersed while playing the first Deus Ex and felt like I was a part of the game world, in Invisible War I felt like the world is fake because all the maps are way too small. This is also the reason exploring the game world wasn't fun but tedious for me.
Human Revolution is overrated. After I beat the first Deus Ex, I beat like 10 more times and also played lots of mods for it. After I beat Human Revolution the only thought I had before uninstalling the game was 'I've seen everything this game has to offer' and never wanted to play it again. It doesn't help that the plot is basically rehashed from the first game just like in Invisible War.