Ikaruga is implied to be a mainline sequel. The Stone-Like Being shows up as the final boss. The exact same one from Radiant Silvergun. Killing it permanently, ends the time loop for good. Though you don't need to know what's going on to enjoy the game.
Speaking of Treasure, Dynamite Heady. I do recommend Gunstar Heroes and Gunstar Super Heroes. Super Heroes is a sequel, but at the same time, is a glorified remake with a much deeper story line, when playing on the harder modes.
Ristar is a pretty good one-off.