So here's a question for all you veteran Freespace players. Space flight sims are my favorite genre of game probably of all time, I played much of the Wing Commander series as well as Tie Fighter and X-Wing vs. Tie Fighter but sadly I missed Freespace and Freespace 2, untill now. So my question is, from a story stand point, do I need to start with Freespace and play through that before I play Freespace 2 or are the storys largely unrelated? I plan to play both eventually, Im just curious if I need to start with 1 to understand the story in 2.

I haven't started FS2 yet, but from what i've read i think that, storywise, it works basically like the Wing Commander series: previous titles gives you a bit of insight about the general lore, but are not really needed to understand the current plot (also unlike WC there are even less, if any, recurring characters in FS)

You don't need to start FS1 first to understand FS2 story. And you can read about the general lore in the FS2 database (in-game) . Hovewer it is more logical to start with FS1 - the way it's supposed to be. (you don't want to spoil the FS1 story, right?)

BTW, the best way to start with Freespace is to buy FS2, install FS2 Open and MediaVP's, download Freespace Port and then play the original FS1 campaign using the latest graphical improvements.
http://www.gog.com/en/forum/freespace_series/quick_and_simple_freespace_2_scp_installation_guide
http://www.hard-light.net/wiki/index.php/FreeSpace_Port
http://www.hard-light.net/forums/index.php?topic=70941.0

Oh the plan has always been to use the updated graphics, I just wanted to know if I should be particularly concerned with the order in which I play them, as my friend has talked up Freespace 2 to such a level that Im sorely tempted to skip the first and jump right in to the second if the story doesn't count on your having played the first to know whats going on.

You can safely play through FS2 campaign and jump to FS1 later. The most important things you need to know are explained in the intro and debriefings. Enjoy FS2 and install FS1 campaign mod later. I did that and I am not feeling bad about it. :')

I don't really agree with the general opinion here : I think you should play both episodes chronologically. The general consensus among FS players is that FS1 has the best story, and FS2 the best engine and gameplay. Now that you can play FSport, which is basically FS1 campaign with Freespace Open engine (based on FS2 engine), I think you should start with that.

Another reason to start with FS1 is the technological progression in-game. If you start with FS1, you'll start with low-tech fighters, and once you get to know them you'll be given additionnal subsystems and more exotic weapons to play with. This is an efficient way to maintain interest in the game and to vary the gameplay. Then, when you'll switch to FS2 campaign, you'll be able to see new capital ships with new weapons that strongly change the way major battles are fought.
If you go FS2 then FS1, you'll just feel that FS1 gameplay is lacking some depth because it does not give you as many tactical options as FS2.

For me, you should experience the two campaigns in order, as the developers intended them to be experienced.

I agree with Nnexxus. Official FS campaigns should be played in chronological order. FS1 -> Silent Threat -> FS2.

I find Silent Threat Reborn more worthy of a playthrough than the original Silent Threat, but yes, playing ST before FS2 is a good idea. However, if you really want to jump directly from FS1 to FS2, you won't lose much story-wise.

And after FS2, if you want more (and you probably will) I suggest playing Blue Planet. It's, IMHO, the best non-canon continuation of the FS universe.

Well I had started playing FS2 before your comment Nnexxus however I haven't had a lot of time to play yet so Im only 9 missions in and can easily stop and go back to FS1, I guess the real deciding factor here will be how long it takes me to get FS1 downloaded and FS Port working. Or do I even need to get a retail version of FS1 to run FS Port?

No, you technically do not "need" FS1 in order to run the port. But it's nice to support such a good franchise, isn't it? :') (recommended Reborn version of Silent Threat expansion campaign).
http://fsport.hard-light.net/website/

I don't mind supporting the franchise at all, I'm talking more from a "how do I set this up?" stand point. And might I add OldEnt that your guide on getting FS2 working with the updated graphics was excellent. =)

If you have already managed to set up the FreeSpace 2 Open (v.3.6.12) and the latest graphics upgrade (MediaVPs 3.6.12) then it would be very easy to set up the FreeSpace Port and Silent Threat: Reborn. Just download these files:
http://fsport.freespacemods.net/releases/fsport3_2-complete.7z
http://fsport.freespacemods.net/releases/fsport-str.zip
http://fsport.freespacemods.net/releases/fsport-str-voice.zip
and follow these instructions:

"Unpack the 'FSPort Complete' package into your FS2 directory, and it should create new subfolders for FSPort and FSPort_mediavps. Then select either of those folders from the MOD tab of the Launcher.
If you are using the FSPort Media VPs, be sure that you have the official FreeSpace 2 3.6.12 MediaVPs installed in 'mediavps_3612' and you're using FSO 3.6.12 Final or newer.

You must select a Ported campaign in the campaign room such as "The Main FreeSpace Campaign" or "Silent Threat". Simply launching into the ready room will start the main FreeSpace 2 campaign, which will not work when the Port is active. You must also use a separate pilot for FSPort campaigns or you will encounter strange errors." (HLP. "FreeSpace Port 3.2 + FSPort Media VPs 3.6.12 Release!")

I have really enjoyed FS Port now that I have had time to really get in and do some playing. Im on Good Luck and I've encountered a problem. As best I can tell the Ursas sent with me to take out the reactors fired off all their bombs at fighters in the previous mission for reasons I cannot fathom. Is there a way for me to stop them from doing that or is this a bug because using nothing but cannons they simply cannot take the reactors out before being killed. (And no, they aren't getting killed by fighters, they actually live a long time just not long enough when using nothing but cannons) I even looked up a video of the mission on youtube but the youtube video was just doing what I did only his Ursas still had their bombs.

EDIT: I went to the the Hard-Light forums and looked, it is in fact a bug that the bombers don't seem to use their bombs in the FSPort version of the game, something screwy with their AI.

Yeah, this is a known problem. I did not encounter it myself, when I last played FSport about 8 months ago using 3.6.10 build. Maybe you could try with 3.6.10 exe and mediaVPs, instead of the latest 3.6.12 which I assume you're using right now.
I believe that your pilot file will work directly with 3.6.10 so you don't have to restart the campaign. Can't be sure though, so I suggest making a backup of your pilot file first, just in case something goes wrong.