If you can find a cheap flight into Hanoi it might be a good place for a logical first stop. Starting at the northernmost point and working south, even if you have to wind around here and there, makes more sense. If you fly into BKK, you'll have to make it to Hanoi and double back but sure you can take a different route and see more. May not be a big deal for you though. Have you compared flights between landing in Hanoi and in BKK? I know BKK is cheaper but it might not be a very significant difference.
From Hanoi you can plan your trip a number of different ways. There are more border crossings now then there used to be too which makes overland travel a lot easier and more convenient. BTW, Halong Bay is stunning. One of my favorites in SEA.
It sounds like you're focusing on Vietnam and Cambodia? Do you have planned stops in Laos and Thailand or are just traveling through? Asking because a very nice trip is north to south Vietnam and then into Cambodia. On your way out of Cambodia you could travel southern Thailand and hit some beaches if you're into it. Or, easily travel in and around Bangkok if you're interested.
Bangkok is busy. Hanoi is busy. Both can be overwhelming if you've never been. There's lots going on in both places. I wouldn't necessarily gauge my flight on which is easier if you know what I mean
