Well, from my view, SFC2/OP is the better game. It has more depth, and overall gameplay. Yes, it has it's own issues, but SFC3 was majorly underdeveloped, imo.
SFC3, to my mind, is also no more Trek than SFC2 is. The arcs aren't representative of Trek, in fact if anything SFC2 has more Trek like arcs than SFC3, as well as many other facets of the game. The Tactical was taken down too far, and whereas I like the addition of some of the elements (reverse and warp are fun), I certainly don't think they were adequate replacements for the elements that were taken out. All weapons are fairly the same, SFC2 requires that you use many of it's weapons in much different fashions than eachother.
SFC2 has much more racial flavor, even in the screens. I think the move to one universal UI was a big mistake. It also has much more variety in missions. I agree with Atrahasis, that SFC3 lacked vision. To me, the game was lacking in almost every area. It seemed like a game made for the sake of making a game, rather than a real passion, or love for Trek. I don't think much effort was put into doing research on the era, what the ships were like. And there was certainly very little creativity put into filling the holes that Trek has, in order to make it a well rounded game. While I'm not a proponent of the ship building aspect of things (I just don't think a starfleet would operate that way, and I prefer the upgrade system from SFC1) it seems to be to have been halfway done. More thrown together than well thought out, and the variety of systems is very lacking.
I say this, as someone who was really looking forward to SFC3. I even put up a website early on dispelling some of the bad rumours running around and trying to bring some people into the fold. I did begin to worry when I saw some of the posts by a few Taldren employee's that appeared to be grasping at straws when trying to say why SFC3 was going to be so good and why SFC2 was so bad or "stupid". Still I looked forward to it. I was so pumped when I got the disk I didn't even go to work that day, unfortunately I was so very, very disappointed in the final product. It could have been so much better, but it fell far short of even SFC2 standards, imo.
Yes, it has prettier graphics to a certain degree (my geforce2mx makes them look rather drab unless you zoom in sometimes) but the gameplay is just too lacking. I figure the only way I'll go back to SFC3 is if I make some type of mod for it, but everytime I start to think about it and plan some ideas, I start remember all the things the game can't do. It's unfortunate. I could go on about it, but for me SFC2/OP will have to do, despite it's many problems. I had really hoped that there would be a successor to it that would really amp things up (and SFB doesn't matter to me, just deep/quality gameplay, in case anyone is lookin' to throw a label).
btw, when I play SFC OP (I don't actually play EAW, and haven't for years now) I only use 3 fingers and my thumb on the keyboard. The rest I do with the mouse, and I do just fine. I leave my fingers sitting on the 1,2,3 buttons and the thumb on the Z. Only occassionally will I use the B button. I guess I never understood the whole "this game is too complex" thing. Unfortunately SFC3 seemed to have solved a lot of "problems" by just removing things. Fewer tactical elements equals fewer keys I guess. Trouble getting fighter AI to work right? Just remove fighters, etc. I really would have loved to see Runabouts launched out of starbases and stuff, but alas that much Trek was not meant to be, I guess. To tell you the truth I find a lot of Trek games lacking in Trek, and it's sad, especially when other franchises do a fairly good job emulating the universes they are from.