” not being allowed to daven Mincha just because that is what the commander decided”
Actually, the halachah is that if your employer doesn’t give you the time off, it is asur to daven minchah! You can probably make it up with tashlumin; consult an IDF rav.
“being told to do things that are mechalal Shabbos”
IDF being mechalah Shabat in many if not most cases would be pikuach nefesh. We learned this one the hard way with the Maccabees as they originally decided not to fight on Shabat, and got massacred.
“the army does not go out of the way to get mehadrin food”
So eat the non-mehadrin food! When you are in the IDF you no longer follow the halachic rulings of the community you are from; you follow the IDF’s rulings. And you don’t call your former rav to ask whether you should obey an order.
That said, the IDF really should do more to respect the religious traditions of all soldiers. Even though many rabbis (including mine) are meikel on kol isha, there was no excuse for prohibiting frum soldiers from quietly excusing themselves when a female singer was performing. Ten minutes for a minchah minyan should rarely be an issue unless someone is shooting at us. And Rabbinut Mehadrin food is readily available throughout Israel; why can’t the IDF offer it? The IDF has well qualified Orthodox rabbis; why can’t it follow them?