How come command points are not on the cards?

A valid point, and an oversight on our part. We should have included Command Capacity on the ship cards, and didn't.

How come there are not cards for all ships, I mean, including the shuttles and escape pods, or even missles?

Shuttles, pods and missiles were considered simple enough (no special rules, very basic capabilities) as not to require a data card.

Also, how much value does the TOS have if you aren't using the advanced orders loss?

It's also the place where you keep track of add-ins (the modchip/insert setup), and track the actual damage level of each vessel, and in some cases keep track of the current orders and order status (such as which skirmish squadrons are in "berserker spin" mode and which aren't).

Orders Loss is hardly the sole reason for the TOS.

Personally, I keep thinking that there must be some way to play the game using cards and not the TOS.

It might be possible, but it wasn't designed to be used that way. The TOS is intended to be an integrated, essential part of the recordkeeping for the game.

How come the Carrier gets like 8 command points? It does cushion the fleet from orders loss, but to me it doesn't make sense that it would need 4 orders to repair 4 squadrons of ships.

Different opinions for different people. It made sense to us when we set it up that way. If you'd prefer to reduce the Carrier to a command capacity of 5 and make one "repair fighters" switch to cover all four bays, that's a perfectly valid house rule.

Also, I feel that the orders are very internal to the ship. It seems very strange to think they could loose orders. Loosing the capacity to do things due to damage makes sense to me. Making it flip back and forth between ship capabilities doesn't make sense to me, especially when they start with the ability to do it all. (Perhaps, I'm asking the 'reality' question which isn't fair of any game.)

Probably it's the reality question. The idea of Orders Loss isn't to simulate loss of capability (that's what the powerloss/damaged/crippled's effects do). It's to simulate the chaos of a battle. Hectic, heavy fighting, commands being garbled by communications equipment, captains panicing and making mistakes.

A player, sitting in his own home, eating a bag of chips (with his off hand) while programming his turn at his leasure is far less likely to make errors than someone who's in the heat of battle, ship blowing up around him. So the Orders Loss rule is intended to help simulate this.

when are you coming out with Electronic Warfare ships which degrade the order capacity of a ship?

Early designs included this capability on the Control Corvette, and for reasons I can't get into, it was removed. We will consider means to directly attack the command capacity of a vessel in future expansions.