I already posted what I thought on the thread involving his characterization and focus, I say he is not getting proper limelight. My thoughts rest there, but I'll lay down my thoughts...
You got a great actor voicing Raphael in Sean Astin, a decent design with a thunderbolt scar largely in the unknowing and establish a pet in Spike and rivals like Xever. At first glance, season 1 and 2 balance him as the straight man in the house of "freaks"; often Raphael is balanced alongside the group. Normally, whenever he isn't the center of attention, his aggressive tone and sarcasm give Raph wit towards the situation. It also helps Raphael played the main hero in one of my personal favorite episodes "Slash and Destroy", further establishing a future conflict with the mutated Slash, originally Spike. So the potential is there with receiving opportunities, but then the holes are poked...
Season 3 butchers the character immensely beyond the saving grace the first two seasons left. Raphael was turned into a plant during "Within the Woods", turned into the Shredder's lackey in "Clash of the Mutanimals" for a brief stint, injured for no inexplicable reason in "Attack of the Mega Shredder!" and so on. Combine that in with him being the butt of the jokes as a so called "straight man" or middle child if you will. In addition, Raph also suffered a bit in season 2 where he was swapped with a Kraang in "Plan 10", turned into a turkey head in Mazes & Mutants", Karai spits in only
his eyes in "Vengeance is Mine", unable to ride a horse in "Turtles in Time", and the space thing which I don't harbor a grudge here. See the problem?
Furthermore, name me one time in season 3 where he got actual focus alone in comparison to Leo, Don, and Mike. As far as I'm aware, it was only twice in the season, which were somewhat a balance in "Casey Jones vs. the Underworld" and taking limelight at the end of the season in "Dinosaurs Seen in Sewers!" Even if both are among the season's best, why did it take until the end of the season for a stand alone Raphael storyline; as far as I'm concerned one actual episode out of 26 is poor. That's how I see it, Raphael's balance has been off since the middle of season 2, making him a victim which shouldn't be his character. Add in a lackluster relationship with Mona and so far, it's not great for the character.
If Raphael is meant to be this tough guy, making him a sissy and unable to fight 8 times out of 10 and always suffering is poor handling. It's like my problem with this interpretation of Michelangelo being a goofball; these two are more than simply aggressive and goofball respectively, they are who they are in other version and both are adored. As far as I'm concerned, the horrible handling of both is painful to view, and ultimately as a Raph fan you're going to be

a lot.
You mean like Mikey being a goofball in the Croaking for no reason after late season 2 development? Or Leo's injury inconsistent? Raph being a bigger wuss?
Season 3 murdered these characters both in writing and handling. Seth, Rob, Greg, and Sean do excellent in these roles, but there's no way I see them handled that good after season 2 besides Leo.