its akin to arguing dallas vs houston. neither are great destinations. both dirty, overpopulated cities, and the 'attractions' (hoan kiem, pagoda, opera house, etc) are a bit light on gravity.
they should be experienced once, and if its a matter of either/or, then saigon has more of the hustle-bustle, beehive-moto-traffic one imagines of vietnam. and the food is much better. (hanoi, however, has access to balong/bai tu long bay which is a cannot-miss).
the real 'gem' of the country (someone used that word in this thread) are in between..... in hue, da nang, da lat, etc..... with better natural geography, more room to roam.
flights are really cheap from point to point, whether by discount carrier or the national carrier. even the best class of service on the national train (violette carriage - 4 bed sleeper), isnt comfortable, has limited availability, and takes an interminably long time.