how'd you mean?

If you charge > stop to throw then yes you have the -1 to shoot. If you stand still for the entire move phase then no, you can use your standard shoot value with no penalty.

The only real advantage of the Thrown Weapon was that you throw it on the charge. In the shoot phase it's just a short range weapon with no other advantage (ok, you don't loose shield ability with it but is that really worth the points and 6" range vs. a dedicate bowman???).

I really think GW should have had an exclusion to the -1 penalty for using a Thrown Weapon on the charge. They are a lot less cumbersome than a bow/crossbow/etc., which you can justify the -1 for. This is, so far, the only "Fail" I have personally found with the updated rules.

I don't think that any up grade should be free. I only give Mordor orcs bows if they have already got spears, so they have the option of shooting from behind an orc with a shield etc, usually when I have a few points to spare.

As was already stated, I see no reason to take Warg Riders with throwing spears when they'll only hit on a 6 and cannot be used if the Orc dismounts.

I am not worried by the rule per se as it makes sense in real terms as remaining stationary should be more accurate

I can't fully agree with that, because when not actually aiming through a visor and all that, it takes me just as much time to nock an arrow, pull the string and release while directing it at a specific target, as it would to do the same but in some random direction. I.e.: aiming doesn't add any time. Besides, proper bows used in warfare are way to heavy to actually hold strained for any amount of time