I actually much prefer "Honor Thy Father". Portnoy, it seems, managed to harness his aggression and frustration in a manner that translated into a well-written song. So often reactive/reactionary sorts of tracks tend to come off as uninspired and forced, as though the writer wanted to make an attack more than they wanted to make a quality song. This doesn't appear to be the case on "HTF"; sure, aggression has been poured into this track, but a great degree of thought has also gone into it. The result: one terrific piece of heavy progressive metal.
Now, "The Best of Times" I don't care for much at all. Yes, it's sweet, and yes, it's a nice song, but I've got some major gripes with it. A) it's not very interesting, musically, and b) it's ridiculously drawn out and overblown without there being much variation at all. The track is repetitive, it's excessive, and it quite simply has no business being 13 minutes long. Ultimately, this results in a rather poor song overall.