Ya know, that got me as well when Orion Pirates came out;  I couldn't tell from the box if I could play the old races AND the pirate races.  You can play one's precious federation in OP is you so wish.  It's what I do, and the added pirates give a lot more to shoot at.
As has been mentioned before, in SFC3 the 'excelcior' model is a mediocore class at best (As I don't have the SFC3, I can only tell you what others are saying;  I have no proof of this myself)  However, in Orion Pirates, the 'excelcior' model is used for the Federation's battlecruisers, which are highly popular and powerful creatures.  (As I have Orion Pirates I can attest to the Federation's battlecruisers being both popular and powerful.)
The tatical complexity of OP, EAW and SFC1 may disagree with you if you find SFC3 a handful;  However, there are set difficulty levels (captian, commodore, and admiral) and you have fully customizable skirmishes where one can improve their skills.  In addition for those willing to read a little to improve their skills, there are large volumes of player-compiled tactics online.  I believe battleclinic is the most relivant to SFC 3.
For those truly seeking glory however, player to player battles can make the game's artifical intelligence look poor, slow, and stupid;  For a real rush, playing the old hands here can be very... educational.
I recommend Orion Pirates;  It has the widest selection of gameplay (which gives challange for both new and old), is still easily available, and has a cadre of people of high caliber willing to put the time and effort to make it better;  Taldren is yet working on one more patch for the game, and people such as Firesoul, 'Evil' Dave/Tracy/Karnak, and many others continue to work dilligently on making improvements, such as firesoul's OP+ shiplist and mission conversions, or the Evil Three's Mission Packs.
Take a captain's chair, grab a cup of your Empire's Beverage of Choice, and enjoy youself;  If you have any questions, we'll try our best.
Holocat.