I complained loudly about my sniper because in PvE and getting killed all the time. Primarily because Kaliyo is a horrible tank. But after taking some advice and changing my play style a little I have found my Sniper is very effective PvE both solo and grouped (especially grouped).
My Sniper is lvl 27 and primarily Marksman tree. The defense buffs to cover (and breaking cover) are awesome.
Here are some keys that helped me (I am no expert so feel free to correct any errors)
1. Kaliyo is a horrible tank, she can't take much damage. So I usually keep her in offense stance (it reduces her threat generation), so that she can remain alive the entire fight. I also turn off her Distract (taunt) skill and save it for when I am low on heath (remember you can manually trigger these abilities)
2. We don't have any long term Crowd Control, but we have lots of good short term. If anyone ever gets near me I Deabilitating strike them. If i'm getting too much heat from a group (or even one mob) use a flashbang and focus them down one at a time.
3. Remap the take cover keybind. By default your chracter will roll to the nearest cover, you can remap it so that automatically goes to cover where you stand instead of rolling (or you can use Shift+F). This made a huge differnce, once i disovered how powerful cover was and started using it more (cover - move - cover), i realized what a liability rolling around was, when I want cover I want it were I am at.
4. Balistic Dampeners (marksman tree, teir 2), this like a powershield, only better. 100% chance to absorb 30% damage against 3 attacks (and it has a buff icon so you know when it expires). I believe this is in addition to the default bonus provided by cover.
5. Snapshot (marksman tree teir 3), allows snipe to activate instantly when taking cover. This is great for pusing out a lot of burst damage, and when combined with Balistic Dapeners you stand/move then go back into cover now you have refreshed your Balastic Dapeners and get and instant snipe shot.
6. In long fights keep your Energy bar above 50% (actually 60%) to maintain good energy regeneration. In case you were not aware, the higher your energy bar the faster you regenerate energy, very important. It is easy to burnout on expensive shots, but you need to manage your energy to keep your sustained DPS up.
Like the sniper says in TF2 Have a plan to kill everyone you meet.
I like to open every battle with Ambush since it has a long activation and cooldown. I also like to use Explosive Probe right away since it is high damage, this gives me just enough time to squeeze off a 'fee' (not activation time) snipe, by this time Strongs enemies should ready for a TakeDown Shot (lvl 18 skill).
I will admit that unlike my Powertech and Sorcerer, my Sniper is not good (or even able in some cases) to solo a Champion (platinum enemy) but here is how I like to handle other enemies.
3-4 normal enemies - practice a rotation, I like to exparament, sometimes using AoE, sometimes dps them down one at a time. these should not pose a problem.
2 normal + strong - Here you want a plan. using the strategy I described above you should be able to quickly solo down the strong while directign Kaliyo to engage the normals. Alternatively you can have Kaliyo engage the strong while you dps down the normals then assist her.
2 strong (silver) - you take one, Kaliyo takes one. (again you can burn them down fast with the above strat).
1 Elite (gold) - Elite vary enough that you may need to adjust your strategy, some are more resiliant or do more damage than others. Things to remember. 1) Refersh your Dampeners 2) occassionally have Kaliyo distract (taunt) to take heat off you. 3) use deabiliting strike or flashbang to give yourself time to activate Ambush. watch for them to use a special ability and interupt it with a stun or distraction (especially heals) 4) finally my filler attack for Elites is usually snipe and explosive probe when it is available.
1 Elite + 1 Strong - have Kaliyo engage the elite while you burn down the strong then assist.
2+ Elite - now you are in the heroic arena and proably need an ally since Sniper doesn't have long-term crowd control (unless they are droids, then you have slice droid)