I'm very sorry.  This post is an epic fail so far, so I am basically quarentening it until I can actually type something that can actually make sense.  This edit is being placed far above to ensure that nobody believes all of this post until further notice.

Sure, they have all those heavy cruisers, but if you can think on your feet (er, engine), you can easily take down anything anybody throws at you.  This guide's sections are based on scenarios, so you actually know what situation I'm talking about.

1.  You're just about to siege an enemy planet.  You have about 70 ships, a fleet to be envied so early in the game.  Then, your jaw drops to the floor when you see not only a huge enemy fleet, but also 20 gauss turrets close to your position.  You attack, hoping for the best, but those turrets just hand your hind over on a silver platter before the enemy's actual ships get a chance to take you down.  You lose all those ships, and your enemy has a chance to siege your weakened empire.

Solutions:  Okay, two problems; your fleet is destroyed, and your enemy has a chance to swoop in and take you down faster than you can say uncle.  So, what caused this problem?  Do you have any long range frigates?  If you don't, I'm very surprised.  LRFs are the most often spammed ships along with HCs!  So, sorry to be so blunt, but build them!  If you do, you're probably not using them at a long range.  What did you think they were made for, going toe-to-toe with cap ships (not recommended...)?  If the turrets are a short stone's throw away, you'll have to get your LRFs away from them (along with your other ships, so they don't get damaged).  Secondly, your empire is weakened if you fail.  That's why you should only attempt this size siege when you get later through the game.  Sending all of your ships will leave you defenseless.  Also, this would not have happened if you at least retreated! (Warning:  those who are stubborn should not play this game at the risk of not retreating and getting your butt handed to you.  You've been warned... )

2.  Yet again, you have a huge fleet.  You now have every kind of ship in your fleet.  Ninety ships, and you've got frigates and turrets defending all of your planets.  You go in for the siege, but only a quarter of your fleet reaches the enemy planet for a while.  When the first quarter of your fleet gets picked off, the next quarter goes in and is beat down.  By now, your fleet is quite a few ships short of a good fleet (literally) and, instead of retreating, you go in anyway, thinking you can take them.  They slam you against the edge of the gravity well, so you lost yet another fleet.  What a waste....

Solutions:  There are three mistakes here, but im only revealing two.  Anybody who guesses the third correctly can play against me online.  Anyway, first mistake (in order of importance, least to most) is that this guy didn't retreat (see end of first solution).  If you retreat, you can live to fight another, er, minute ("day" would be inaccurate).  Second mistake, your ships went in wave by wave.  If you planned to do this, shame on you.  That's about the dumbest thing to do besides spamming cielos and not having any other ships (I sure hope NOBODY does this!) Anyway, sending in waves will just make you look like an idiot.  Remember, this game is no Saturday morning cartoon!  However, if you didn't plan this, your ships probably aren't using group movement.  To turn on group movement, right-click the move button.  This will make it so that your ships jump at the same time, and get somewhere at the same time.

3.  Oh boy, at 200 ships in your fleet, you must be unstoppable.  You go in to siege the enemy planet.  All your ships get there at the same time.  You make sure your long range frigates are out of harm's way.  However, your LFs get taken down for no apparent reason.  Your LRFs finally start firing, but it was too late.  Most of your fleet is downed, and you have to retreat.

Solutions:  You may be thinking "that can't happen!  The enemy fleet should have been taken down!"  However, this can happen.  The LRFs were taking too long to start firing.  Because of that, only half the fleet was active.  They ended up getting destroyed because of a lack of immediate support.  At least this guy retreated

4.  You're too impatient to wait for a bunch of ships to be constructed, so you spam a fleet of scouts.  There are many scouts in your fleet, so it looks like you're set to go.  Unfortunately, you don't have anything to bomb planets with, so you just decide to take down there ships and structures instead.  You go in for the attack, having twice the number of ships as your opponent.  However, your fleet of scouts gets gutted like a turkey the night before Thanksgiving dinner.  Better luck next time, suckers!

Solutions: Obviously, don't spam scouts.  Sure, make one or two scouts to explore the system (HIGHLY recommended) or to take out a structure with some timed explosives (BOOM!), but they're just not meant to go toe-to-toe with other ships.  They have more than half the fleet supply of an LF, and still have under 1/3 of an LF's average power (more than 1/3 when considering the Advent, but still), shoddy armor, and a low firing range to top it all off, so a group of 30 fighters can take out a couple scouts before the scouts get there.  Besides, they aren't strong against anything, so why even bother?

Well, you can be sure that I'll add to this guide later, so don't have kittens if you don't see much here.  Thnx for reading, and I hope learned something and laughed along the way.