- The pilot would be in danger the more he piloted the mech suit.
- The pilot was male.
- I believe it had a space setting.
- It was probably also on Cartoon Network / Toonami.
With not much to go on, is there any chance it's Tekkaman Blade, also known as Teknoman?
The main character transforms into a white power-suit, but there was a time limit on how long he could spend in it.
Much of the story took place in space.
It came out in 1992, although I think it was dubbed into English around 1995-6, and it doesn't look like it aired on Toonami.
the anime you're thinking of might be "Blue Gender." "Blue Gender" is a sci-fi anime that aired in the late 90s and early 2000s, and it involves mechs known as "Armored Sleeves."
In "Blue Gender," the main character, Yuji Kaido, pilots an armored suit to fight against giant insect-like creatures called the Blue. The more a pilot uses the suit, the more they are at risk of a condition called "Blue" sickness, which can be life-threatening.