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I am not fully sold on it being better to go first in ship battles.  

Phase 3 Pilot phase, there are some places where first is better but most are not.  One example would be if ship A and B are 2CU apart and A going first stays where it is then B gets the chance to make sure its weapons are in range or the other ships are not.  Same goes for if ship A closes ship B moves away.  The advantage of going first is if you want to run.  

Phase 4 sensors.  If ship A locks on ship B, B can now try to break the lock.  If ship B tries to lock there is nothing A can do about it. Yes if ship A does a pulse it is better to go first.  But under locking its far better to be 2nd

Phase 5 attacks.  Its good to attack first to do damage and crits but bad for defensive items.  At 2 CU there is no way for ship A to defend against a torpedo launched that round.  A takes a turn then B fires torpedo and it hits same round.  But if A fired then B would have a chance to counter.  The second in initiative has the advantage by if the other ship does not launch one then they know they can fire other weapons with that EP.

Thoughts?

Hiya, bit of a long one, sorry
You present some good concerns in regards to space combat, and it’s all plausible, but there are some other factors to also consider in each area. These mostly have to do with strategy and a mix of bluffs and good (or bad) dice rolls.
The piloting phase allows each side to maneuver to the best position for the rest of the round. Yes, going second might give you a chance to put some distance between both ships, but doing so negates the ability to evade incoming attacks from the first player. Since weapons have a max range but not a minimum, for combat purposes it’s in the player 1’s advantage to get as close as possible, since running away is based on total successes of the running (2^nd) player. Of course the reverse also applies, if the first player closes distance, the ability to avoid player 2’s attacks is given up. When it comes to straight up running and chasing, going first or second plays less importance as “hiding” from the enemy comes down to sensor operator rolls. So long as that chasing pilot can keep within scan range, not much will change.
The same thing basically applies to sensor operations. Player 2 can spend his one action breaking the target lock, but then loses the ability to lock his own target, can’t try to hide, and can’t send meme attacks. Breaking target locks also only give a -2 to the other players ranged attacks while disabling his ability to use torps, both players would be at this disadvantage and it probably will happen this way often.
When it comes to torps closer than 2 AU away, the hit is indeed the same round as it was fired, but the targeted ship does have the option of defensive fire with auto cannons or countermeasures. These are considered to hit the torpedo at the last second, saving the ship from damage, but at the cost of the regular attack that round, provided the target player held his attack action for such a case. Normally, you would either attack or wait for that suspected torpedo, but you can’t do both. It comes down to who has an active lock and who doesn’t since torpedoes require it, as well as dice rolls to hit and all that. The other thing in all this I would note is that if Player A was holding his action waiting for B to fire a torp, and B never does, A would waste his combat turn waiting. A gamble, yes, but without a limitation both sides would just keep “holding” their action indefinitely. Of course, if you have extra gunners everything changes J
I don’t know if it really answers your questions/concerns, but after playing around a bit with it, it didn’t seem too biased going first or second. More about your crew plotting and scheming to get the best advantages in the fight and working together.

You make some really good points. I never thought of holding actions. How would you handle it if both hold actions?

In most games I've run over the years, the rule has been similar to the Overwatch rule here; the action is held until a chosen event or condition occurs. If it doesn't happen, the held action is spent waiting and the next round starts. A is waiting for B to fire, and B is waiting for A, both stare intently at the other with a finger on the button. An adjusted ruling could be, after each side has held their action once, starting at the top of the list, each must choose to either hold  or attack and at the end of the second cycle the round is over. This would play out as waiting for the enemy to do something and then having to make that quick decision to either keep waiting or simply act. I prefer to not do this though as it's almost like adding a second round of turns for 1 or 2 players. If you hold your action, you take your chances

I think that is a good way to handle it.  Where if you dont attack you can hold for defensive but you can NOT hold to attack

Do you know when you roll to hit with a torpedo?  Is it only the round it is going to hit?  For example if someone fires from 4CU you would not roll to attack until next round when it goes the 4 CU and then you roll to attack at the same time as the autocannon?  Or would you see if the torpedo attack worked then use the autocannon?

Hrm.. good question. I think it would need to be rolled at the time of launch, that way you wouldn't forget to include any bonuses from commander if applicable. The target would be able to see that they are about to be hit in X rounds and could prepare in whatever way (brace for impact, plan to use defensive fire, etc). When the torp is launched the calculations for hit are made (the number being put to the side until contact and damage occur) and it's basically on it's own after that, aside from the lock I would rule still needs to be on the target ship. If it was going 6 AU, then by the third round the gunner would be using other weapons to attack with while his torpedo strikes home as a free action. Well.. that or launching more torpedoes heh.
Thoughts?

You brought up some good points. If it was fired at long range 4cu and moves 2cu per turn then the target ship could keep moving away and delay it more. I would say if the torpedo was locked it should stay locked. Also rolling then makes sense like you said due to captain bonuses and lock bonuses. I guess the target ship just knows if its going to hit or not and how well.

Yes - roll for torpedoes at launch.