Out of all the nit picks and bitches about separation of Church and State though, I think this is the most legitimate.
I disagree. It's "an" issue to nit over, but not the most "legitimate". At least not if by "legitimate" we mean the degree to which it's actually in violation of the 1st amendment, upon which the principle of Separation of Church and State rests. The 1st amendment specifically forbids congress from passing laws respecting an establishment of religion. Obviously, this has been extended to "all levels of government", but still applies to the passage of laws (so legislature).
The change of the US motto from "E Pluribus Unum" to "In God We Trust" can clearly be argued to be a violation of that amendment, but the placing of those words on our coins, ironically, is not. Those words were placed on US coins long before Congress changed the motto (motto changed in 1956, but "In God We Trust" has been on US currency since 1864. The reason the words on our coins is not a violation of the 1st amendment is because the words and symbols on the coins are at the discretion of the Secretary of Treasury. While Congress passed a law *allowing* the Secretary to do so (basically giving up Congressional control over what coins could say), currently it's up to that Secretary, and thus it arguably not in violation of the 1st amendment.
Are we talking about loopholes here? Sure. But that's what makes this not be the most legitimate of nits to pick on this issue. All the other side has to say is "there's no law requiring those words be on our coins", and the case is more or less closed.
This would be nice, but it doesn't seem like such a big deal to me. At least not compared to some of the other things, like "under god" in the pledge they make school kids say every day...
This is a vastly more legitimate one. The public school system is established and funded by act of congress. The requirement for the pledge to be spoken was created by act of congress. And the words that are to be included in the pledge to be spoken are also established by act of congress. It's about as clear cut a violation of the principle at hand as you could get. I'd start there if you want to really make headway on this issue. Of course, all that has to be done to fix this is for congress to pass a law leaving the pledge decision up to the individual schools or districts, and walk away from it. Then you have to go fight each school and convince them to change their policies if you don't like it. Which may be more trouble than it's worth.