Ah, nothing like a good argument to start off the day!

Of course I made up my mind that FS1 is better. I don't see how that's your argument, it IS better than FS2 in my opinion, so...what's the point of your argument?
That's exactly the problem, and it causes you to be irrationally biased. Look at your arguments in support of sm2-04a.fs1 and compare it with those against sm2-03.fs2. You are frequently holding exactly the same thing against an FS2 mission which you praised for an FS1 mission. I bet if the missions were exactly the same but only the games were switched around, you would suddenly start saying great things about that mission just because it in FS1.

However one thing you missed. While the Alexander mission was a crucial part of the story, what with the avenger you use constantly afterwards (and some hidden stuff), the stealth test mission was just one random gimmick designed to make you occupied (and of course the protect mission was repeated again afterwards just before you join the lions, kind of to be another filler mission). As much to my recollection, I used the Valkyrie a lot in fs2, never touched the Pegasus after that test. Hell I didn't even fly IT in the test. It's like the thing never existed. When was stealth good? When you went to scan the juggernaught, wowee, where have I seen THAT before? At least in fs1 it was a challenge, the copy of it in fs2 was just blah...
Here we go again. I could just as easily say that the whole McCarthy thing was "just another gimmick designed to make you occupied." Now one thing about the Valkyrie; that was the first
combat test of the Valkyrie, not the first
controlled test. It had probably been tested many times already and had passed all its testing, so this is the first time it is being used; essentially, this amounts to getting another ship in your pool, so this is no big thing as far as the mission goes. (or if it is, you might as well say that every mission in which a new fighter is available is crucial to the story) The Pegasus on the other hand was being tested for the first time and had a whole new capability.
I will agree that sm3-05.fs2 was very similar to this one. However, you have no room to talk on similarity of missions, since there must have been four or so FS1 missions where you had to raid a cargo depot and another three freighter convoy defense missions (containing stuff you would use later on). FS2's missions were much, much more varied, and this is evidence by the game reviews.
And disable the tiamat? Why would I do that? the thing gets nuked without me disabling it, I just gotta keep it within my sensor range...that's as much to my recollection, I can go play it again if you want me to check. Sorry I usually just sleep through that mission, what with all the piece of **** primaries value, I can sleep and spam my missiles and win...
No, not disable it completely, but get rid of the Shivan Cluster launchers on it so that the AIs don't die right away. It helps in that one. I would also like to have a disabling mission or two in FS2, which had too few of them, but FS1 had a bit too many.
Yes, you are right that the better primaries come after that (right next mission, in fact), but you get the tempests which, while technically a secondary, are used exactly like primaries.
The....Hammer and the Anvil...
....That mission is one of the more important ones you do...according to this guide thing, anyway, it's the one where you're escorting the shield prototypes on a route toward earth, if you don't call that important, god knows, what matters to you, but yeah, you see a point in stealth, somehow....
Look, all they really are is cargo containers with labels. The shields themselves don't play any role in the mission at all; they could all be exchanged with Bosch Beer for example and the mission would be exactly the same. The one interesting thing about this mission is that incident with the PVFr Andromeda, but that alone is not enough to make an essential story mission.
The Aftermath
This is debatable... I believe it's there to hammer home the Tombaugh station's loss, does pretty good job too IMHO... heh, fighters chattering, a delicate and huge convoy that needs to defend. I also think it's the first one you're almost fully incharge of stuff (....That winds me up to no end, AI dying because I can't order them....).
Come on, if you give it that much leeway just about every mission has some tiny little thing in the story. Is it interesting and fun? Sure. Essential to the story? Not really.
The Big Bang introduces red alerts, also you're defending the Tsunami project, which, dunno about you, but I use rather a lot later on, nuts to harbinger... (apart from for luci), admittedly, it's not desperately plot important, but it helps, most of the techs come out of no where, especially in FS2.
Once again, this is just labeling a cargo container (or a science cruiser in this case) with some important thing and cannot alone be used to make the mission a story-advancement mission; in the mission itself, there is no tsunami used. Heck, this kind of thing could be used to "justify" the importance of sm2-01.fs2, where the cargo is the TAG missiles. (otherwise it is a pretty standard escort mission and one of FS2's fillers)
As for the FS2 comment, that's because they are being developed back at the main systems while you are at the front lines of battle, so they are ready to go by the time you recieve them.
Fortuna a filler?
Read the command briefing before it, wont be so filler...
The fact that it's infested with shivan's makes you wonder, considering previously, and throughout the rest of the campaign they seem to very very losely work together.
A command briefing alone is no substitute for a mission story. Yes, it was surprising that the HOL outpost was gone and the player was not initially expecting a fight with the shivans, but that alone does not make it anywhere near an essential story mission. If you just keep the command briefing and change around the whole mission, the overall story will remain more or less the same.
Where Eagles Dare - Same as Fortuna, read the command briefing.
See above.
Well, I could put up no arguement, I mean, it's not exactly the most prophetic mission in the game, however there's something about the Eva just having engaged it's subspace drives as you get there that makes me wanna say it's there to increase player tension or something similar, considering it teases you in a 'can't touch this' style...
Sure, I felt the same thing, but once again, this is not nearly enough to have a true story-advancement part in the mission.
Yep you're right, and another minus point is how lame it was done
Well, like its tech description says, it is not quite as powerful as any GTVA corvette and is probably used for different purposes, so there was no point in trying to show off its power.