Using an arcade controller isn't too different from a gamepad aside from the lack of twin stick controls, so there isn't anything to worry about for this game.
Anyways, have you thought about doing linear platforming stages in the style of Metal Slug or Sonic? It would allow for interesting challenges like speed or no-damage runs to add more depth to the game mechanics. The paths could go up, down, left, right, or anything between for varied stage design. You can look up GMTK on YouTube if you want more inspiration.