I chose Aldynes. Even though the graphics are somewhat generic and its gameplay system was nothing particularly innovative at the time, its gameplay is nonetheless the most perfectly tuned. Enemy behavior and placement, enemy size and speed, bullet size and speed, control of your ship, your weapons and supports, and more; there's nothing that I would change.
Aldynes has awesome music too, and otherwise good atmosphere, so I don't think it has any real weaknesses.
Sometimes when I die in TFIV, I get this feeling like they were actively trying to piss me off. When I die in Aldynes, I feel humble, like I let the game down. That's why I wind up respecting Aldynes more.
TFIV has amazing graphics, and one of my all-time favorite Genesis soundtracks, but playing it really stresses me out sometimes.