While I do not think this applies to most or all of our fleet. Considering how helpful and informative we are. I still feel the need to post this out of my own experience with nonfleeties and for any future additions to our fleet. As it will be helpful starting out and not going in blind I think.
Borg Red Alert
Goals: Destroy 4 groups of borg ships. Then destroy borg mothership.
This one is pretty direct and most groups have no problem with it, except maybe the borg mothership on rare occasions.
For the first part I would suggest staying away from tactical cubes, they look like normal cubes with grey armor. I would say go after normal cubes. At most they travel in pairs and their pretty slow moving, so as long as you don't give them time or split your attention they will go down without much trouble. Just remember not to get to close as they can tractor beam you as well when the blow that can hurt if not kill you outright. Which happens more often then you think due to their sheer size and ability to creep up while your blasting away. I would also suggest going after cubes with spheres, focusing on the cube before spheres. Again cubes are easier to deal with then even spheres so long as you don't ignore them. Spheres tend to strip your shields fast but their attack is not as strong as cubes. Going after large groups of spheres is strangely enough pretty dangerous due to numbers and their shield stripping. Unless they have probes mixed in, in which case focus on probes first as their pretty weak in comparison and cutting down the numbers is always a good idea.
Once four groups go down their will be a cut scene to the mothership. This bad boy is huge and has little buddies. Here you basically have two options. Full on focus assault or spread it out. Personally I do a mix by focusing on the big boy while throwing in a multi target attack such as fire at will. You can and most do make it a dps race with the enemies ability to heal itself. But if this is not working for your group then you can strip the enemies defenses and ability to heal by targeting it's little friends. Two things you have to be mindful besides breaking through it's defenses. Are it's ability to spit out probes, if you take to long and focus to much you may find your being outnumbered. So you may want to pay attention. The other more pressing and dangerous one is it's giant torpedo, not joking this thing is bigger then your ship unless your driving a big boy yourself. If your shields are low or just not good enough this torpedo will almost every time one shot you. Lucky for you it's slow so as long as you don't hung around it's mouth at point blank range you can shoot it down without much trouble.
Tholian Red Alert
Another pretty direct red alert, still I have seen it failed more then a few times. Most often due to lack of team work or underestimating the big bugs.
The tholians are split into a few big groups with borg thrown in here and there along with a pair of dreadnoughts. Don't worry unless your pretty fast the bugs wipe out the borg with in the first minute or two of the red alert. Consider them swarms as that is what they are. As such they will and do bleed into each other. It's best to start at the edges and destroy them as you go deeper. If you dive right in then odds are your a dead duck and don't know it yet. Tholians have beam weapons that bounce off each other and drain your shields which is why getting into the thick of things is so hazardous. Another thing you have to worry about with the blue boys is their webs. They will use them to cage you and running into them does hurt you. Break out quick by targeting the nodes that make up their corners as it's not uncommon for the dreadnoughts to blast you while trapped. Even if you don't get blasted the cages while expire and crush you if your inside causing damage. The webs block line of sight as well so you won't be helping anyone while inside too.
As far as ships are concerned you have to keep an eye on the dreadnoughts. You can ignore them or target them but ether way you have to stick with it. The dreadnoughts are not only powerful and tough, they spit out mesh weavers. Those little guys are not the tiny fighters you ignore because their little pop guns won't even give you an itch. No those little guys have bite and your going to feel it if you let them go. The mesh weavers main purpose is to swarm you with their shield draining bouncing beams, those hits add up and so does the damage to both your shields and hull. Putting those guys aside the dreadnoughts have a powerful and wide blast ability. Yes it takes time to charge and the graphic will let you know it's coming but it still packs a lot of punch and should be avoided. For ships without good defense they will get one shotted, if you do manage to survive them you get trapped in a mini web without being able to do anything but use hull and shield healing abilities. If the dreadnoughts are close to one another or facing opposite directions it's not uncommon for them to layer or blast at the same time increasing the area. Only the toughest ships will survive layered blast.
All that said when you take on the dreadnoughts. Make sure your team is focusing on one and paying attention to any near by ships. You have to keep the number of smaller ships manageable and focus on one dreadnought at a time. Splitting your team between dreadnoughts is never a good idea and will make things harder. This red alert like all of them is timed, they don't need to beat you. Just eat up your time.
Tzenkethi Red Alert
Goals:Protect the planet from protomatter torpedoes and destroy the tzenkethi dreadnought
The most complex and often failed red alert. Lack of awareness and team work being the cause. Also not having at least one multi target ability ready.
This red alert has a few stages and even options to earn a bonus to your regular reward. At the start you have to protect two satellites from the tzenkethi. They are a limited number of waves on the satellites you have to defend, once you destroy enough they stop. The waves come in trio's, one cruiser and two frigates. Focus on the cruiser as it has the ability to make others immune to damage for a time, this ability is not limited to ships. So they can protect protomatter bombs that pass by which is why you have to destroy them first and pay attention to any passing bombs. As time passes the tzenkathi torpedo boats show up and start firing a string of protomatter bombs. The bombs are easy to destroy but if your not careful the sheer number becomes unmanageable without effort, which is why you should always have a multi target ability going into this red alert such as fire at will. This is the stage where most teams fail. Many abandon the satellites which not only help destroy passing protomatter bombs but are also the subject of the bonus. Which again have a limited number of enemy waves to deal with. They focus on destroying the torpedo boats instead and the bombs just sneak by or become to much for back row ships to handle. It only takes a single bomb making it to the planet to fail the red alert. Now if the team remains at the satellites and passes the waves then the enemy no longer attacks the satellites leaving you free to move your way up towards the boats. While the boats will not move, they have cruisers and frigates with them. Again the cruisers are a priority due to their protection ability. Once the bomb boats are destroyed a dreadnought appears with some friends.
This is another point where teams often fail. The dreadnought fires protomatter bombs as well. If your not paying attention they will sneak by you or get lost in the fireworks of focus fire. Take out all the small fries and stay on bomb look out before and during this last stage of destroying the dreadnought to pass the red alert. If you properly protected the satellites then you even get a bonus. Also as a side note both the boats and dreadnought have a focus missile ability that will show up as a red filled circle near or on your ship, move away from it quickly to avoid a hard hit. The closer you are to the ships the faster you have to move, they hurt alot but only target an area not ships.
Well that's it. Feel free to post your own tips or any corrections to my own post. :)