Changes to make Crawl harder
Remove teleport control and -cTele
I think the case for this is self-evident; if scrolls of blinking are really too good without -cTele, surely they should be nerfed everywhere instead of just on 2% of levels. Even if you don't change blinking this is a difficulty increase everywhere that isn't zot:5.
Remove ring of teleportation and *Tele property
Unlimited teleport leads to grindy behaviour (because of things like water, vaults that have to be teleported into...) and makes consumable teleport awkward on top of that. Admittedly this is an unnoticeably slight difficulty increase.
Remove or nerf lantern of shadows
Aside from the horrible interface screw, finding this item makes pretty much the whole game (more) trivial. It is downright embarrassing that it has been like this for so long. Rod of shadows is ridiculously overpowered, sure, but at least it doesn't give you a free cloud of powerful summons that regenerates even when you are constantly moving. It needs to either go away outright, or at least consume MP/HP when wielded (but every character in the game would still carry it so that's not enough imo).
Nerf elemental invokers, probably sack of spiders
These are not nearly as egregiously insane as lantern of shadows, but they are very common and a large part why it's a no-brainer to get evocations skill on every character ever. Sack of spiders is less ridiculous than it used to be but elemental invokers are as bad as ever. I know the stacking removal was meant to nerf them, but you don't use a whole bunch of invokers in a single fight anyway. My suggestion here is to at least make them rarer, and if the stacking change stays, using an invoker should deplete all invokers of any type, instead of just all invokers of that type. I know that takes stone of tremors from basically useless to completely useless if you have any other invoker, but it's still an improvement over the status quo imo. (I know there's not a shadow of a chance of getting them removed.)
Don't start deep dwarves with a wand of heal wounds
Again the rationale for this is pretty obvious, starting a character with unlimited heal wounds destroys all pretense of difficulty and on turn 0 to boot. Even in the worst case (DDAK) early game is trivial.
Remove zombies, skeletons, goliath beetles, water/lava monsters from natural monster generation (and appropriate vaults)
They're free XP and piety, especially noticeable early game. Worms too but I discovered some people have an attachment to those.