I'm contemplating running an Only War game via play by post and since I have not GMed any of the 40k RPGs before I was thinking of using one of the published adventure supplements to help me. So I want to know which one I should use. Is one regarded as better than the other? Is one better for a starting group? What sorts of enemies would a Regiment face in each?

I really like the first third of No Surrender.

Zero-G, No-Air combat. Attacking a massive space station filled with Severan Dominate.

But I'd probably change the second and third chapters.

Spoiler:

It's Chaos.

I'd change them to something different. Have an attacking Ork fleet. Have the severan surrender. Convince them that the Duke is a meanie.

Just not the spoiler

Personally, I like No Surrender. It can be played from the perspective of either faction quite easily, and it's a really cool scenario to play, both with the Big Bad who shall not be named herein, and the need to play intelligently when taking into account the hazards and functions of a Space Station. I found Final Testament quite dull to run in comparison.

I will say though that No Surrender has a much harder endgame, whereas Final Testament has a harder early game, although the Dominate can be far more dangerous if played intelligently by the GM.

A greater variety in opposition is never a bad thing, however. Consider, for example, the use of Dark or Craftworld Eldar in either story playing the various factions against one another. (See Rogue Trader's Koronus Bestiary or Dark Heresy's Creatures Anaethema for Craftworld Eldar statblocks.)

In Final Testament, it could be revealed that the planet is a Tomb World, awoken by major plot event X. Or perhaps a Tyranid Hive Fleet stumbles into the sector; I'm pretty sure Moloch isn't all that far away.

The only real problem you're likely to experience in terms of writing a faction in is the Tau, as they're so concentrated in-universe, though there is an Enclave in the relatively nearby Koronus Expanse that you could use, or the gate to the Jericho Reach. (unless you just want to move the game to the Jericho Reach in it's entirety.)

This game provides such a rich base of options you can play with to mix things up and make it interesting. All depends on how comfortable you are, and your creativity.