I think the biggest weakness in both this adventure and most of WotC's adventures is encounter design.
Some encounter design is really cool, like the vampire spawn in the attic in Curse of Strahd. Other encounter design, like the fireballing wizard in the 2nd level DiA dungeon could use some work.
Likewise, it is very easy to make your adventure more internally consistent when writing it. For example, the Alexandrian points out the hydra issue. For many people, this isn't a problem. But by adding just a line or two of text about how/what it eats, or mentioning that it is starving and eating its own heads, can add a lot and give the DM more to work with despite the slightness of the addition.
These two things combine to turn me off of many WotC adventures. I either feel like my encounters could be way more interesting or that a little more cohesiveness would have a force multiplying effect on the adventure. Neither of these things are a big ask. Again, for the Hydra, one or two lines would suffice. For the adventure hooks, why not look at the adventure itself and program them in, or even wait on making them until the main book is finished?
When I look at other 3rd party adventures, I get these things. Indie creators and 3rd party studios go the extra mile on their products to make them cohesive and the encounters interesting. As a game designer myself, there's really no reason to not do these things. It doesn't take more effort, it just takes a bit of vision.
And for a game that's as focused on exploring hostile places as D&D, I'd expect these two elements to be superb in every adventure. That it's not is disappointing.
I do agree many of WotC's adventures, including this one, have great ideas in them. The mutations, the weird cow, even the idea of Mindflayers hunting down the obelisk I like a lot. DiA had many good ideas I've stolen, as has every book WotC has put out (even Spelljammer had some goodies I liked). But I'm not just buying these books to steal ideas. I'm buying these books to experience high-quality encounters and to receive coherent materials.
There really isn't a valid argument against this IMO. WotC just needs to try harder. They have the capability to be one of the best in the business, if not the best. What's so wrong with pushing them to do better?