All these changes do is homogenize stuff and reduce functions for no other reason than that they take a bit of thought to play with.
No. None of the changes were made for that reason, and the fact that you're misrepresenting them is silly considering that the reasoning for every commit is generally spelled out. In any case, how exactly do dietary requirements "take a bit of thought"? All it does is make you chop up slightly more or fewer corpses, and that process is either directly automated or mentally automated for almost all players.
We've already discussed item destruction but I'll say that the Nemelex changes and the reasons for changing him are a lot more complicated than you're making out. The god in its old form had a lot of problems that made it frustrating to use (mindlessly sacrifice everything on the floor, deck weighting system was incredibly opaque, have to read spoilers to know how to deal with each deck, once spoilers were read you knew which decks to mindlessly draw and which decks to mindlessly triple draw, decks wasted tonnes of inventory space which made managing them a chore) and you should be happy that they're making a serious attempt to reform him (with new cards and deck dynamics) rather than just taking him out.
I enjoy that extra challenge of working with the fast yet vegetarian diet of centaurs, but now they just play exactly like a fast high elf. I don't find that fun at all.
Sorry but I actually laughed out loud at this. The vegetarian diet/fast metabolism did absolutely nothing other than make you have to chop up corpses more often. Centaurs did not starve to death under the old system. The idea that they're remotely like High Elves is also ridiculous. Speed and HP are the two most important distinguishing factors for vanilla species, and centaurs beat the shit out of high elves on both counts (that's why they're an incredibly strong race). Then there's also the fact that their defenses and apts are entirely different... I'm actually struggling to think of similarities beyond "They can both used ranged combat quite well".
You have most of those "fundamental" decisions in your basic RPGs though. Why would you want to turn a Roguelike into one of them?
This is an arrogant and elitist view to take, and also it makes no sense because "basic" RPGs can include food systems, item destruction and limited resources. Maybe "basic" RPGs do some things right? Dungeon Crawl will still maintain all the actually interesting parts of being a roguelike so who cares?
Roguelikes have alway been about managing limited resources (which is where food and item destruction come in), as well as heaving various abilities to screw the player over unless he knows how to deal with them or has the means to do so.
You'll still have to manage limited resources - the number of items you can use is limited by the number of items you have found, and this has always been the important limit. If item destruction really was massively reducing the number of items available in the game then that can be easily fixed by reducing the spawn rate of scrolls/potions.
It will take some balancing, but food under the new system may actually feel like managing a limited resource eventually (a thing which it has never succeeded in being in the past). See: Spriggans.