That's a very keen observation that I'd not thought about until now, but would agree with... especially since I'm one of those people that have HBP as their favourite book (probably) and PoA as their least favourite xD I think you're right on the mark.
They're very different books, I feel. Maybe because of the relative lack of evil characters (the only book we didn't even see Voldemort in) in PoA compared to the abundance in HBP. One of the things I adored in HBP is that the evil characters became less one-dimensional. We got an insight into the going-ons of Bellatrix, Narcissa and Snape (in his Death Eater persona) with the सेकंड chapter, "Spinners End". With Dumbledore's lessons throughout the novel, we learnt और about Voldemort- his motivations, his childhood, his past misdeeds. We got to empathise with Draco as he was forced into their cult, and it was the first time we saw a side of him besides "mean bully-boy". Adversaries weren't just adversaries "for the sake of it" anymore- they were much और well-rounded. On the whole, it was quite focused on characters, and maybe not so much plot (which I loved about it).
Compare this to PoA where there was just plot, to the expense of character development (I feel). It was much और 'black-and-white' in the divisions- the trio, predictably, played heroics, two obvious 'good-guys' were introduced in the form of Lupin and Sirius. Wormtail was the only contact we get with a "baddie" and probably the least-compelling one in the whole series. Much और one-dimensional characters, no exploration of their motives/histories/nature, running purely on the excitement of the "scary prisoner escapes from Azkaban and is coming to get you" and Time-Turner themes. I found it engrossing at the time but it's not something आप go back and read, as आप can do with HBP.
That's my take on it, from personal experience. Not sure if it makes much sense. But this सवाल is a very good pick-up on your behalf, and very true :)
Also I just realised why I've always disliked Sirius, Lupin and the Marauders in general. Probably because they were introduced/most associated with PoA and held those connotations for the rest of the series.