Short Answer:

Yes, other than the ending, it's not as close to flawless as season 1. But you still need to watch it.

Long answer (Spoiler Warning):

Everyone talks about how much season 2 sucked compared to the first season. While it certainly wasn't terrible, it really could have handled itself better. The writers put in unnecessary try-hard plot twists that just ruined the story.
For example:-

• The death of Nunally. I think the death of Nunally would have added a lot of meaning to how Lelouch loses everything in exchange for power, but then of course the writers pulled the totally unnecessary "haha she's alive" card. Tbh, I kinda predicted that she was alive. When a character as important as her dies, they wouldn't make it that quick. While she was disintegrating from the FLEIJA explosion, they would have shown what was going on in her mind at that moment, and things would have been in slow-motion. But her death just happened in a second, so it wasn't really a surprise.

• Even the death of his mother. There was absolutely no need to make it that she was actually alive but her "conscious" was put into another person. After all, her death was one of the driving forces of the Black Rebellion.

• I also did not like that they did not show the origins of the power of Geass. Who made the Sword of Akasha? Why is there a planet while they were standing there? What was that army of people with Geass symbols on their heads that Lelouch saw when he got his Geass?

• The scene where Suzaku attacked the UFN meeting for the vote to add Brittania as a member on Lelouch's orders also did not make sense. If Lelouch wanted the peaceful world Nunally and Euphemia wished for, he wouldn't have tried to make the UFN vote for him by force. Even if it was the dream of the most important person to him in the world, Lelouch is not monkey-brained enough to achieve that by coercion.

But, Well, in the end, all these questionable plot turns were required for the flawless ending. I mean, it makes up for it and more. The moment you see Zero running towards Lelouch, you already know what's going to happen. Seeing Lelouch sacrifice himself for the sake of the world was beautiful and touching and all the previous things that happened seemed insignificant. The scene where Nunally held his hands as he dies reminded me of how important siblings are and how much of an impact they can have on each other. It's probably the best ending of any anime I have seen so far. Trust me, it's worth it.

So the best thing to do is to look at the series as a whole, not season 1 and season 2. Then it will be easier to look past the plot holes and just enjoy the show for all the good sides.

I think the best analogy for season 2 is by Gigguk from the anime podcast Trash Taste:
"Season 2 was a car crash that somehow perfectly parallel parked"