The reason that Alec gets very little insight into what Jace is feeling through their parabatai bond is because Jace, being a classic Byronic Hero, is such a constant, roiling mass of Mangst that it is almost impossible to sense the difference between Jace-in-life-threatening-danger or Jace-quietly-reading-a-book-in-his-bedroom.
This answer would make sense except that the parabatai bond rarely ever seems to work for any pair.
Just realized what if the extra angel blood Clary and Jace had enhanced the skills they already possessed. That would partially explain Clary's potential to create new runes, and Jace working so hard to earn his Valentine's approval when he was a kid would explain him being able to jump out of a Malachi configuration.
Except Clary isn't actually creating new runes. It's stated in City of Glass that Ithuriel is showing the runes to Clary and continues to do so.
In City of Lost Souls it's stated the rune Clary uses to destroy the inter-dimensional apartment is not one that had already existed, and was completely new. New to her anyway. The Alliance, Portal and Channel Heavenly Fire runes were also completely unknown to the Nephilim until Clary introduced them. Even the Silent Brothers acknowledge that they only know a children's book worth of words from the language of Heaven, and have absolutely no idea as to how the vocabulary and syntax of that language really works.
That Valentine took the angel blood that he fed to the pregnant Jocelyn from Ithuriel would account for why Ithuriel seemingly has a Psychic Link to Clary, but not to all the Shadowhunters. The rest carry Raziel's blood. Clary's prenatal exposure to Ithuriel's blood gives him a connection to her. But her mind was closed to him for most of her life because of Magnus's elaborate Laser-Guided Amnesia spell, which also limited the Silent Brothers' telepathic access to her mind even at close range and while working in concert. Notably, Ithuriel starts having more influence on Clary around the time that the spell begins to wear off because Magnus is no longer renewing it. Jace developed a more physical enhancement because he was always pressured to be a perfect warrior, and his willful agnosticism and emotional issues might have made him harder to reach mentally. Even his parabatai bond with Alec was very limited as compared to some other such pairs.
The success of the demonic siege on Alicante, and the fact that nowhere in the city was safe, might seem odd at first. But given their Nay-Theist tendencies, the Nephilim do not actually have any places of worship within the entire country of Idris! There is basically no hallowed ground, just the magical wards created by the towers and localized wards made using runes. The Shadowhunters have a very utilitarian mentality when it comes to religious symbolism. For example, using such symbols against vampires. They probably also had very limited supplies of things like holy water, since they normally obtain that from allies among mundane religions. Believing that Idris and Alicante were utterly secure, there would probably have been less of it in the whole country than there is stockpiled in most Institutes in mundane cities and lacking any kind of clergy they could not produce it as needed.
When you realize that the bad guy (Valentine) got the Shadowhunter funeral and the two people he hurt the most (Amatis, Celine) are buried as outcast dead, which means their spirits can't move on. (It makes more sense if you've read The Infernal Devices.
The Shadowhunters' excuse for that is that they didn't want to risk Valentine coming back again. As for Celine she committed suicide and supposedly didn't deserve a respectful death. Yeah... (For extra Fridge Horror its hinted that Celine was killed and the murderer made it look like it was suicide. How's that for messed up?)