The whole post-Thessia dialogue is poorly done. First, Shepard is blaming herself for the loss (WTF?) and everyone is saying "its not your fault" then suddenly, Liara is blaming herself and Shepard (if interrupt taken) says "stop blaming yourself." There's no continuity here. Just lots of attempts to pull at heart strings, but no real sense of how these things fit together.
I also found the writing on Liara's reaction to Banshees to be over-the-top. She keeps freaking out that Asari have been turned into husks, but has never once evinced any concerns about blowing away husks from other races. Again with the feelz, logic take a back seat.
I don't get her reaction to Prothean intervention on Thessia either. She knows quite well the Protheans have been intervening with other races. Is it any surprise they intervened with hers? Again, go for the feels, not logical continuity.
Finally, Javik's claim that the Protheans gave the Asari biotics is another poke-in-the-eye at established lore about everything living thing on Thessia having biotics. Once Javik claimed that Asari biotics were the result of Prothean intervention I basically discounted everything else he said as a lie.
Over and over in ME3 the writers showed they only cared about spectacle and feelz and the devil take logic and sense. Perhaps this is because there are so many writers. If there was just one writer then you might not get all of these problems, though even the best writers can still leave you with gaping, huge plot holes. (So, why didn't the eagles fly the ring to Mount Doom, anyway?)
Because the eagles could never get close with the watchful eye of Sauron?
I believe you are being a little bit overly-harsh and critical of a part of the story that could have potentially been handled better, but wasn't terrible.
Shepard isn't necessarily sad about Thessia going up in flames, although he certainly wasn't happy about it. In truth, it was the Asari who were to blame for failure to join the rest of the galaxy and ignore the reaper threat because of centuries old divisions with the krogan. What Shepard was angry about was losing to Kai Leng, who obtained the prothean VI, which was the galaxy's last shot at figuring out what "the Catalyst" was.
Liara, on the contrary, is upset about Thessia. She, for obvious reasons, is an Asari, and she is also the Shadow Broker. With so much power and resources at her fingertips, I too would be a little upset if I didn't do more to avert an impending doom upon my planet. Wouldn't you be upset if everything you ever knew or cared about was destroyed and you felt like you could have possibly made a difference to stop it?
Liara empathizes with Garrus about Palaven and Shepard about Earth. She can never be truly upset, however, until the horrendous acts are actually hitting closer to home. Seeing the banshees. Seeing Thessia being destroyed. These are tangible things that impact her as an Asari and as an individual.
Liara and the Asari had a very unrealistic outlook of what the Protheans actually were. She essentially worshiped them like gods without ever truly knowing them, and the Asari also just believed they were superior to the other organics in the galaxy. They found the Citadel. They were the first Council race. They were the leaders of the government and had lifespans far exceeding anyone else. Such realizations eventually will go to one's head.
Why would Javik lie? What purpose would he gain? He was merely blunt and willing to state exactly how things were. I found his direct approach to be rather illuminating.
Anything to do with the main story was all Mac Walters. The other writers were either writing the story for the various companions or creating side missions. I truly believe ME3 was the best out of the trilogy, and had the most heart-warming and tragic story we have seen in a very long time in the video game industry. It wasn't perfect. It had its flaws, but it was an incredibly gratifying experience and one I can continue to play over and over.