I quite enjoyed season 5, especially with Spike there (I also liked Eve), but something fundamental was definitely always missing without Cordy. I remember watching each new episode as it came out and wondering when there was going to be talk of waking her up and why this wasn't a thing.
I was completely blindsided by what happens in "You're Welcome" and wondered for quite a long time how that could have been the plan from the start.
Clearly, it wasn't.
I really don't get writing her out altogether. She obviously could have been present for season 5 as much as they needed her to be. If it was just because they were mad at her, that's stupid.
Okay, yeah, waiting to "the last minute" to tell them about the pregnancy probably made a big hassle with regard to plans that were already in place, but it's probably a response exactly like this that had her nervous to tell them. Assuming "the last minute" means relative to when she found out and not when prior plans were being established.
If she was quiet about it for weeks and even months before saying, "By the way, I know my character is like this super important figure for the remaining 16 episodes of the season, but I can't do them all," then, yeah, I'd get upset. I wouldn't punish the fans of the show over it, but I'd be upset.
That seems to be where -- in the writing of specific episodes of the season -- Joss found out about the pregnancy, as his DVD commentary for "Spin the Bottle" (episode 6 of season 4) mentions that he already knew Cordelia and Connor would be having sex at some point in the season, but that he then moved the plot point up to the next episode because of Charisma's pregnancy.
So, let's see -- Charisma's son was born March 24, 2003. "Spin the Bottle" aired November 10, 2002, and was probably written/filmed sometime in September or October. As far as I know, the birth of Charisma's son wasn't premature, so conception likely occurred in late June of 2002. She most likely couldn't/wouldn't have known she was pregnant before the last week of July or first week of August, at which point they would already have begun filming season 4 if the July 24 start-date for season 5's filming is anything to go by.
So, there's somewhere between one and two months where she didn't let them know?
That is a sizeable chunk of time not to mention it, I guess.
Still, there was no reason other than spite not to bring her back for season 5. She had returned from maternity leave in time to even be in the last episode of season 4.
I won't go as far as to comment that they could have worked around the pregnancy altogether for season 4, seeing as she was barely there past episode 17 (of 22) and the plan was always that Cordelia had been possessed. As intended, she probably would have been much more of a physical threat to Angel, and it stands to reason that a pregnant Charisma couldn't have done a fight scene as a superbeing.
Even if she could have, maternity leave removing her from those last episodes of the season would have been a problem if she was supposed to be an enemy up to the season finale.
So, yeah, I get being frustrated over how things played out. No excuse, though, for not bringing her back for season 5, and especially no excuse for not letting Charisma know they weren't bringing her back.
I'm willing to pretend parts of canon aren't actually canon, because the show just wasn't right without Cordelia.
I don't know how much of the comics you've read, but be prepared to do that a lot.