First Installment Wins: While the later games weren't bad, the first game is often seen as the best in the series.
Goddamned Bats: Not as bad in this series as in some, but there are still some minor enemies that can mess you up very badly if you're not careful, especially the literal bats of RKA 2, which show up in an area filled with hazards and can ruin your trajectory. One in particular appears during an optional sequence where you have to outrun an Advancing Wall of Doom; if you do anything but very carefully fly past it through the narrow gap available, without stopping to kill it, you die.
Nightmare Fuel: The (nearly) unstoppable pigs in the fifth level that chase Sparkster and can kill him in one hit if they touch him.
That One Boss: In the SNES version of Sparkster, we have Axle Gear in his giant mech. Aside from the fact that it's an Unexpected Gameplay Change within an Unexpected Gameplay Change (Sparkster jumps into a giant mech of his own solely for the purpose of this one boss), Axle is unbelievably aggressive, especially on the higher difficulty levels. And he can take a lot more damage than you can. Getting hits in on Axle without getting hit yourself can be nearly impossible at times. Worse, you can't just sit back and block all day, because his punches will destroy your arms over time if you allow them to (you can actually do this to him, too, but it's very hard to do so).
In the first game, the boss of the fifth level counts for this, considering that it's a giant mecha fight between Sparkster and Axel Gear, and Axle Gear can take twice as much damage as you can which makes this a very tough fight.
Also the space battleship boss of the sixth level in the first game considering that it has a lot of health, and multiple phases that you have to defeat in succession.
That One Level: The fifth level in the first game, which was long, had multiple One-Hit KO's in the forms of both spiked enemies and spiked backgrounds, and to top it all off, you had to defeat That One Boss at the end of it.
They Changed It, Now It Sucks: Quite a few fans seem to have complained about certain differences in gameplay mechanics between RKA 2 and the other two games: The Razor Wind attack is gone, replaced by a relatively slow sword slash; the rocket charges automatically as opposed to manually and does so much more quickly, making it possible to stay aloft indefinitely; and the controls are less fast-paced in general. The graphics were also less "hand-drawn" and more blocky, which along with the change in color palette has resulted in the game's visuals being very evocative of Sonic the Hedgehog.
Tough Act to Follow: The original game for the Genesis is considered the tough act for the franchise. Many agree its sequels, while not bad, don't reach its greatness.