Here's my opinion as a big Deus Ex fan: Human Revolution is better.
It's hard to explain why Invisible War is a lower quality title without comparing it to the other Deus Ex games, but it's clear Human Revolution was the stronger overall effort.
Invisible War certainly had it's strengths. It had great graphics for its time, it had some cool in-game gadgets, there was a decent amount of "freedom" and the conversation trees later in the game were really good, and the fan service really piles up toward the end of the game. However, levels were smaller and primarily corridors, the stealth system was broken, the RPG elements were reversible, the story doesn't get affected by your actions, side-quests become inconsequential, everything feels like it was focus-grouped to hell and back. Still a good game overall, but fell short of DX1 and DX3. It also fell short of developer Ion Storm's next title, Thief 3.
Meanwhile, Human Revolution felt like a game that had the balls to push players into difficult situations with unclear and difficult decisions, it had a better story, better atmosphere... just an overall better game for reasons I'll let you discover.
Both are certainly worth playing if you are a fan. I've replayed both titles several times.