These may be stupid but I have to ask.

1) If you collide ship A with ship B is ship A able to attack still? (not ship B since bases are touching)

3) See above. Does ship A then have to deal with attacking through an obstable?

2) If two ships have the same pilot skill who moves their ships first? Player with initiative or player without?

1) When 2 ships collide (overlap) they are unable to attack each other, but they are free to attack anything else on their firing arc.

3) Other ships, including enemy ships, are never considered obstacles. Only asteroids (or other things especifically designated as 'obstacle' in any given scenario) have the 'obstacle' properties.

2) Player with initiative always do things first. Moving, Firing and even deploying his ships on the table.

To answer your first question:

Regardless of who did the colliding, ships that are touching each other during the combat phase cannot shoot at each other.

However, they may still attack anyone else in their arcs.

Moreover, if a ship collides with another ship, and then the second ship moves, so long as they are not touching each other during the combat phase, they may still shoot at each other.

To answer your second question (which is labeled as your 3rd for some reason),

Ships are not obstacles.

Asteroids are currently the only obstacles in game. The rules are phrased that way to allow the freedom to use other obstacles in the future.

To answer your third question (which is labeled as your 2nd for some reason),

In the event of tied pilot skill across factions, the player with initiative moves AND attacks first.

In the event of tied pilot skill within the same fleet, their player may choose the order of movement and attack (a fairly large advantage).