Okay, Managed to play the mission and technically I couldn't find much wrong with actually. Which is quite impressive. Usually I find at least a few technical problems. That said there are some issues with balance and aesthetics that I spotted while playing. Once I've gone through the list of what I found wrong with the mission when I played it I'll open up FRED and have a good look around there.
1) I found the mission a little hard. Things were going okay until the mass attack of Shivan forces. I found that I was dealing with far too much at one time after that happened. It seems like 5 wings all appeared at once. You should stagger the arrivals a little to make the mission a little more playable. I never actually managed to get to the end so I'll have to judge that based on the FREDding instead.
Of course this is just my opinion and you should probably get a few more from other people to see if they agree with me.
2) I found the mission goal is a little wordy. Something like "Protect the Julius" or "Protect the Julius Until it Jumps" is enough.
3) I got a message stating that some of the Shivans had gotten away yet I destroyed all three gas miners. It may be that there are other ships around but I never saw them. Consider adding another miner that jumps out as soon as the player gets within a certain distance of it. Alternatively better messages from the Deimos might have the same effect (although in that case you run the risk of the player managing to get to the miners quickly enough to notice that the 4th Rahu the Julius says exists is in fact non-existent).
4) The messages could use a little work as they were a little repetitive. Mix them up a little when you have several that say much the same thing. For instance instead of "I've got a visual on Libra wing, they're Dragon class fighters." followed by "I've got a visual on Cancer wing, they're Mara class fighters", change the latter to "Damn, I've got a new visual on 4 Mara class fighters" etc. It makes the wingmen seem more realistic.
The same goes for the destruction of the Rahu miners.
5) Where's the music?

Both mission and briefing musics were missing.
All in all that's actually a pretty low tally of problems. Now lets see what I find when I open up things in FRED.
1) I noticed the false Traitor Debrief. I assume that means you noticed that game supplies one automatically.

2) Just a minor thing but I noticed in briefing stage 4 you had this
and
-is-destroyed-delay
--0
--Julius
-is-destroyed-delay
--0
--Annatet
which in case you didn't know is basically equivalent to the much simpler
-is-destroyed-delay
--0
--Julius
--Annatet
3) Again another equivalence thing, you have this (simplified) in Leo Retreat When One Destroyed
when
-or
--or
---is-destroyed
----Leo 1
---is-destroyed
----Leo 2
--is-destroyed
---Leo 3
This is equivalent to
or
-is-destroyed
--Leo 1
-is-destroyed
--Leo 2
-is-destroyed
--Leo 3
Just use the add operator option from the pop up menu to add the 3rd is-destroyed-delay SEXP. That said there is an even better way.
when
-or
-percentage-ships-destroyed
--1
--Leo
-percentage-ships-disabled
--1
--Leo
-add-goal etc
Will have the same effect as your first two events in a single event. As soon as more that 1% of Leo wing is destroyed it will trigger, since each ship is worth 33% you'll get that as soon as one is destroyed or disabled.
4) In general I'm seeing a lot of cases where you should be using add operator rather than making a new event. It is more efficient to stick everything that should happen at the same time in one event using it than to have lots of similar events. It also means that you don't run the risk of having only 3 out of 4 events trigger cause you made a mistake in the 4th. Furthermore if you change the trigger you only need to do it once. A good example of this is the Find Annatet- Change IFF to F, Find Annatet- IFF is F= Visable and Find Annatet- Make Escort Ship Events which all could have simply been rolled into a single event called Find Annatet.
5) Your whole failsafe code is rather odd. Personally I'd remove the whole lot unless you can explain to me what you're trying to do there. I suspect that it's the reason why you're not seeing any ships jump out as it's setting some of the ships to self destruct.
6) You probably shouldn't have used Beta or Gamma wing for the other wings. Right from the start of the mission they are visible in the top right corner's wingman health display. You can change the name of the wings that are visible from the Mission Specs Editor->Custom Wing Names. Change those to wing names which don't exist in the mission and that minor problem should vanish. To be honest I suspect an SCP change is required here really as there are times like this one when you do want a ship to appear on the HUD but not for the entire mission.
7) The Alpha 2 Will NOT Survive! is practically useless. It only triggers after several days and it effectively ship-guardian's Alpha 2. Did you want him Guardianed from the start? If so just use when - true as your trigger. In fact I tend to always start my missions with a single event called Initial Events and stick all the mission start stuff in that event.
8) You probably should consider not instantly blowing up the Annatet if the Julius is destroyed. It seems rather forced to me. Allow the mission to continue but simply make the Shivan forces too much to hold back in that case.
9) You should turn trails back on by unticking that box in the mission specs editor. Since this is a nebula mission it turns them off (at least it should do. I could swear I saw them!).
Okay, think I'm done for now. Apart from my complaints this is looking pretty good. With some better balancing this could be a pretty solid mission.