Right I'm not sure what is causing that problem with most edges not displaying after putting the optimize modifier on but one solution I've found is to add a "Turn to Poly" Modifier to the mesh, with it having a "Limit Polygon Size" checked and set to 3, which will then turn the mesh into the state it would be exported to the game in, but note I would recommend no collapsing this into the mesh as it is much harder to work with actual tris as you can't use the loop and ring selections, as well as other things so effectively.
Now if you add the optimize modifier back on you can see that it works now as it should:
And even with only a threshold of 1, your saving 300tris, which is around 7% off the fuselage, but I would recommend a threshold of around 1.4 for this model after doing a few quick trial and errors tests to see which setting optimizes this model the most without deforming it, with also Preserve "Material Boundaries" if you want to keep the edges for the nose but tbh, not sure you need them really? But ye, with a threshold of 1.4 you save
380tris which is almost 10% off the fuselage alone, also taking into account that the optimize modifier tends to miss quite a few things it can optimize, even if it's optimized them on one side of the model it can miss it on the opposite side too so again as I've said before, only use this tool as a reference to see where you can make the optimizations manually yourself for best results, as it also tends to screw up some parts of the model, although main thing it screws up with certainty is the UVs which you don't have any yet so don't have to worry about that but can screw up some of the mesh too.
Anyways you can see from above, lots of places you can optimise the fuselage with keeping its same shape:
Off:
http://i.imgur.com/YUECjIS.jpg
On:
http://i.imgur.com/sBbNe0X.jpg
And things like even the Exocet rack etc have tris/verts they don't need, although keep in mind you will need to fix up your smoothing while optimizing too:
Also something the optimize modifier has missed but these verts are not needed, gotta made sure you check for this sort of thing all around you model.
Also the hardpoints should NOT be welded onto the wings as firstly, there is no chance of them zfighting, since their bottom face is so far away, they don't waste any UV space which could be used by other things since the hole they make in the wings UV is too small to be used by anything else, they screw up the wings smoothing, waste tris and it just makes making the LODs etc much harder, with them also needing to be totally removed in the later LODs which would also expose the UV hole under them which would just be its shadow on the later LOD which is fine. As you can see on the J-10 for example, the hardpoints are just floating mesh on the wing:
Which are then totally removed in its later LODs, just leaving the shadow under them:
The optimize modifier can't pick up on this but your nose also needs quite a bit of optimization since it has the same number of edges leading down to the tip.
Firstly I would recommend backing up your current nose as you might want its shape as not only a refrence for its orignal size etc, but also a good base to make the high poly model on, since I would reocmmend you control the smoothing with baking normals from a HP nose which will then smooth out any issues caused by optimization, like on the blowpipe missile here where it has nothing really in the way of edges to help control its smoothing, it then has a really shadowy tip:
But baking its normals from this HP model:
The smoothing issues are then corrected by its normal
Then going back to your nose, first of all I would recommend collapse down these edge loops as you don't really need them:
Then can collapse down these edges:
And looking at your loops again looks like you can also collapse down this one here:
Can't really do much more to the nose for LOD0 but for the later LODs there is more you can do but don't worry about that for now

But ye, nose looks pretty much the same, might want some parts scaling up a little to match the old size too, but other than that and the smoothing is a bit worse, which can be corrected and look much smoother than it did before with a HP normal bake, its al lgood and much fewer tris
Lasly for now I'm pretty sure unless you've got a source to say otherwise, that the droptank should be totally round, right now its kinda fat
The thins also have a lot of unessary verts etc:
Anyways have a go with that method of adding the turn to poly with max poly size of 3 then adding the optimize modifier on to see where you can optimize your mesh and also look around for other parts that you can modify and improve that I haven't mentioned above and the optimize modifier doesn't pick out either and then post here with your updates
Keep up the good work and hopefully we can have this thing attacking my Frigate soon!
