While I get why people might not like Haruhi as a character, I like Kyon's interactions (read: friction) with her infinitely more than how he interacts with either version of Nagato. Seeing Kyon getting overwhelmed by Haruhi's crazy whimsical attitude and the few occasions where she's the one who's driven into a corner is far more entertaining for me than Nagato acting all flustered every single time he's around. Alternate-reality Nagato is yet another female character that reminds me of Onodera, only she's even more bashful and clumsy around the guy she likes, which is a pretty tall order given how badly Onodera interacts with Raku.
Like, I can find it kind of cute that the girl lacks the self-confidence to get closer to the guy she likes and it does make sense, but I find making that part of her personality so important to define her as a character to be awfully boring. Oddly enough, I guess even the original TMoHS had a similar setup of "host of characters gather around Haruhi and Kyon and help them/show tell each other what they feel for the other", but maybe it was that I liked how everyone would go along with Haruhi's whims until Kyon would eventually oppose her strongly enough to make his stand against her and her god-like level of authority and power.
On the other hand, having a show where every time the girl is about to get closer to the guy something awkward or funny happens that completely kills the mood and derails the situation... that stuff gets boring fast.