It's the SAID principle (Specific Adaptation to Imposed Demands). If you do one type of exercise regularly, your body adapts to use the least amount of energy, which is good if you're trying to win athletic contests but bad if trying to burn the most fat or build the most muscle.
I too have more trouble with interval cycling than interval running. It isn't so much aerobic, as it is lactic acid "burn" in my legs that kills me after only a couple of intervals.
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