My only complain with BotW when i first "end" it where more or less the same than OP... like it was missing something, but that was mostly because this zelda didnt have the usual twist in the storyline dividing the action in two.
From the beggining you have the end of the road clear... This SORT OF got solved with the DLC and the inclusion of the new challenges and the "unknown" 5 beast.
But anyway as that was the price to pay for being able to get to the final boss first if you wanted... i think is sort of an acceptable compromise.
Yeah, we where missing proper dungeons (or caves even), but if you consider the whole, this zelda is more packed with content and subquest than most of them, and most of the twist and storylines are there for you to discover and piece together.
On the whole, the proyect was too big. It could have used many more quest yeah, hyrule is SO GREAT design wise that could easily accept almost anything... yeah, including more dungeons or caves added later xd
Aonuma was the first to say that they were really full of ideas about how to improve the formula, and this was even before release... they got cut off for the launch, but its ok... save them for the next one ^^
Overall, this zelda is great, but its greatness lays in what this brings to the formula with the whole interaction etc. We where missing many things... but thats not something that could not be added for the next title now that they have the machine working so to speak.