I was lucky enough to spend a month in Thailand and 5 weeks in Vietnam last year. I’d definitely go for Vietnam without a doubt. (I also much preferred Laos and Cambodia to Thailand). There are beautiful Thai islands that are less visited by the masses and northern regions are great for hiking, biking and jungle related trips but Vietnam IMO is far more varied and interesting.
In two weeks you could go from Ho Chi Minh up to Hanoi and see the highlights but if I had two weeks there I’d suggest more in the mid and north:
Hanoi for a few days (more picturesque and Ho Chi Minh).
Sapa – Train overnight from Hanoi to Sapa – great trekking there among the still traditional tribes. Can be a bit touristy on some of the trails so ask to hike off the track to the further out areas.
Ninh Binh – national park area with boat trips and hiking/biking.
Halong Bay – boat trips around beautiful cliffs – a must.
Hoi An – one of S.E Asia’s most photogenic towns, great food too – a must.
If you do go to/from Ho Chi Minh these places are great too:
Dalat – Central highland area – further south but there’s a great bike ride from here to Nha Trang (on coast) almost all downhill in mountains on good roads.
Mui Ne – massive red sand dunes, kite surfing, long beaches not necessarily what you expect to see in Vietnam.
Mekong Delta – tunnels from war, lots of war related history, little villages along delta.
All in all far more interesting than lying on a beach full of pissed backpackers!