It depends on which ships you like look wise to be quite honest.
Here is a very BRIEF breakdown of the each race and how each plays in order of easiest to play to hardest (although still very easy) to play.
Aquans: At least one weapon in EVERY arc of fire. Great High damage ratings... meh crit ratings. Excellent beginner armies as they are very forgiving. Fish people. Lots of fast hard to hit ships. Lots of beams and mines - and great SRS (short range ships... fighters bombers ect)
Terrans: Low damage ratings and crit ratings, but one of the very few races to utilize a lot of shield capabilities. Lots of weapon shielding so your weapons do not get worse as badly when you take damage. Great brawler fleet/endgame fleet as their weapons have staying power. 360 weapons coupled with great Starboard port weapons. Also... nukes...
Directorate: Stuck between shield and somewhat hard to hurt. A lot of their weapons are beam weapons (within 10" you can re roll 1's) and use a LOTTTT of biohazard weaponry which poison off crew members. Cyberwarfare weapons which wreck havoc on ships tech (life support, weapons, ect)
Dindrenzi (my first fleet): Giant railguns attached to giant engines. Very fast, very heavily armored (no shield though) and very hard hitting weaponry. Will throw out way more dice to another ship then the other starter set races. Most difficult to play when beginning however due to weapons being heavily forward facing (gets fixed later when you buy more ships to help you flank/cover the sides). Ships will take a beating coming to you though. No starboard port.... can only shoot to one side.
So those are the diff races... you get dindrenzi vs. terrans in one and Aquans vs. Directorate in the other. To be quite honest choose the box set that you like the look of the most. You will soon find that you will have many fleets to play with haha.
Good luck Admiral