First off, this response assumes there is only one slot for a new Asian civ.
Indonesia, IMHO is the better choice for a new civ, for several reasons:
Reason #1: Population: Compare the (modern) populations of the two countries; Indonesia contains ~237 million people (#5 globally), while Vietnam contains only ~88 million people (#13 globally), so an Indonesia civ would represent a much larger portion of the world's population (and customer base,
).
Reason #2: Area: Compare the (modern) areas of the two countries; Indonesia contains ~735,000 square miles/~1,900,000 square kilometers, (#15 globally) , while Vietnam contains only ~127,000 square miles/~312,000 square kilometers (#66 globally) , so an Indonesia civ would represent a much larger portion of the world's area.
Reason #3: Trade Routes: With the expansion's focus on trade routes, Indonesia would be a better civ to take advatage of the new system; all of Indonesia's major empires were thalassocracies (sea-based empires), and they could have a UA based on sea trade (double profit/speed?) and possibly a cargo ship UU with enhanced movement values/defense ability?. Vietnam, at any rate, wasn't known for trade in the same way Indonesia was.
Reason #4: Outside Influences: Vietnam was routinely being attacked by Chinese armies from the north as well as Khmer/Siamese armies from the west, with varying degrees of success against them; while they fared well against their SE Asian neighbors they were controlled for China for a whole millennium. After this, they did establish a long-lived independent kingdom but even then they never achieved a great empire due to continuing attacks from the Chinese and the eventual encroachment of the French. Indonesia, on the other hand, did not succumb to European invaders until the 19th century; yet, while Vietnam struggled under the thumb of the Chinese, the Indonesians established trade empire after trade empire; Medang, Srivijaya, Kediri, Singhasari, Majapahit (the most famous), and finally Banten; all these states were based on trade between the various Indonesian islands.
Reason #5: Playstyle: Indonesia just seems like the better option to me; the idea of a vast archipelago trade empire is awesome (and Polynesia never quite clicked for me in that regard and they're more for
than
). Vietnam seems like just another militaristic civ, and we need no more of those!), while the niche Indonesia fills is one which is sorely lacking in Civ5 (Portugal fills this too, but if we can have so many military civs, two sea trade civs is excusable, and Indonesia could have a whole different spin than Portugal, given the two are worlds apart).
Addendum: Should there be a second Asian civ, The Khazars would be a superior choice, because they bring a land trade element to complement Indonesia's sea trade nicely. They could easily be the 'Silk Road' civ everybody wants, being at a major crossroads between Europe and Asia.