Sniper here.
As a MM, your primary concerns are:
1) Burst DPS on single targets
2) Energy management
3) Protecting your healers and protecting objectives
My typical rotation is as follows: [before battle, I use Laze Target or Target Acquired] Shattershot>Series of Shots>Ambush [a trick here: while ambush is casting, use your explosive probe. It will deploy and explode immediately after Ambush strikes] > Followthrough > Snipe > Series of Shots > Takedown . . .
The key is to mingle your Series of Shots inbetween your big energy spenders. Snipe is your most energy inefficient ability, so use it sparingly. Series of Shots allows you to regain energy while you are dealing damage, so this is a good thing. Typically in a rotation, if you notice that Series of Shots or Ambush are 1-3 seconds from coming back from cooldown, use Rifle Shot instead. This saves energy. The goal should be to keep your energy stores above 50-60%.
In PVP, if you have a pocket healer as a MM sniper, you can easily hit the 400-500k damage mark on a regular basis. Depending on the match, you can approach 70 kills as well. Use your rotation, attack primary targets, and don't waste your abilities or your energy. You and your healer form a symbiotic relationship, so protect him. Tell him to heal you, and you, in turn, should protect him. When you see him getting chased around by bad guys, fire them down. Most of the times in PVP, when the enemy sees a Sniper out in the open with his little shield and bubble, they got bat-crazy trying to kill you at all costs, thinking you are super squishy. This can work to your advantage: have your pocket healer keep you alive while you just blast everything like an automated cannon. The healer will hit 400k+ healing and you will hit 400k+ damage. With practce, of course. (This usually only occurs in long matches, too. Your goal should always be to win, anyway.)
Targets in order of importance:
Healers: 1)Sages/Sorcs are easy kills, but if they have their force bubble, ignore them.
2) Scoundrels/Commandos - These are easy kills, but if you notice that a Smuggler has used his evasion skill, shoot someone else for 4 seconds. MM Sniper's are designed as one of the best counters to Troopers, so when you see Commandos, you should be licking your chops. Burn them down!
3) Vanguards/Mercenaries/Powertechs/Juggs/Guardians - These present a bit more of a challenge, but you should be able to break through their defenses and kill them.
4) Assassins/Sentinels/Marauders/Shadows - As a MM Sniper, these are your worst enemy. 1v1, you can kill them if you don't lose your cool when they get in your face. When you are in the heat of battle, cycle your targets. If you see one of these at full health, don't bother attacking. Chances are, they are using their invulnerability buffs and you will just be wasting your attacks. Wait until healers are dead (or the invulnerability buffs are gone) before you attempt to take one of these down.
Remember, if you are shooting something but not doing any damage, you aren't helping your team. If you aren't defending an objective or attacking a specific target, you aren't doing your job as a sniper. Your orbital strike should always be on cooldown because you should always be throwing it down on nodes or objectives.
Hope these tips help!
Happy hunting,
Sev'ar'usix | Ebon Hawk