It kind of depends. In much of PVE the challenge level isn't greater than that you can play whichever way you enjoy the most. Still, my considerations:

Skillful tier: ballistic dampers (especially) and imperial efficiency are good choices, great for almost all situations. Snap shot is the weakest of the three and doesn't really provide a dps increase since with instant snipe you still have to wait for the global cooldown. I'd consider taking vital regulators (significant amount of self healing is useful in a lot of situations) or calculated pursuit (provides a fair bit of mobility without a great dps loss) instead.

Masterful tier: hold your ground is a good choice, the other two are pretty mediocre. I'd recommend seek cover and reestablish range instead for snare breakers and increased mobility.

Heroic tier: siege bunker is great, almost a must-have for pve above story mode. Defensive safeguards is also a strong choice, with deployed shields being a decent alternative to it depending on if you expect opponents to be close to you. As a third option to these two, tactical retreat is a good choice too, providing a decent self heal and more use from what is already a solid defensive cooldown. Executioner on the other hand is next to useless in comparison, minimal dps increase that can be hard to fit into your rotation. I'd recommend switching it out for pillbox sniper considering the strength of entrench, synergy with siege bunker, seek cover and the established foothold set bonus.

So in short: siege bunker, pillbox sniper and one of defensive safeguards, deployed shields and tactical retreat.