I will be the first to admit that my claims are entirely subjective and that I'm totally holding the games to different standards, but I still stand by them. To begin with, the friendly AI didn't get worse itself, no, but as the games progressed and the enemy AI became more advanced, the problem of having incredibly dumb friendly AI became more and more of an issue. And the Flood did have more of a presence in the first game, but the difference is that their inclusion worked there. They added stakes, and were unique, menacing, and even a little frightening. But in the sequels, when you've got the full might of the military backing you up, and you're no longer trapped on an isolated world with only a handful of other soldiers to help you, they're basically just another hostile faction, one that is particularly unenjoyable to fight. It's no longer a case of, "Run for your lives, the Flood are coming after us!" but instead, "Oh, look, the Flood are here. Let's cut a path through them so we can get where we're going." And I'm not even starting with what looked to be the plant from Little Shop of Horrors that they introduced in Halo 2.
As for the padding, that's probably the most subjective criticism of all, and I won't claim that Halo was perfect in that regard. It's just that it seemed far less annoying to me there. Like I was saying about the Flood, a lot of it probably has to do with the fact that you're trapped on an unfamiliar world and are still immersing yourself in the setting and mysterious lore.