An ability system would be the best solution over than overpowering pure fighting class to balance them with the more powerfull ones that are spell or hybrid spell/fight based.
I'm regularly playing ToME4 these days, and when i manage to be zen and see beyond those unexplainable (as it can occurs even on a completely cleared zone) and very annoying ToME4 engine heavy stutters and slowdowns in some place, i have tons of fun with fighters.
Because the whole ToME leveling system is based on abilities that depend on your class.
Some active, some passive and some sustained, making fighters a real joy to play, learning many new abilities, increasing the power of the ones you have, etc... and learning how to use them in battle to escape some certain death situations.
Those abilities really give fighters classes as much chances to survive as spellcastings/ranged ones, without removing the challenge as there are plenty of ways to die if not carefull enough or with hubris.
But Crawl is using a very different system and makes this solution not possible unless the devs would decide a big rework of the Stone Soup fundamentals as in the current Stone Soup rules, the devs made the choice to have the species being the important choice while the classes have much less influence (explaining why nearly everyone wanting to go far will end in using some magic or godbased spells).
And it would then change the gameplay, something that not every players and devs would appreciate, so it could be a risk for the future of Crawl.
I believe with a class based ability systems, it would have been then possible to make Thief and Death Knight truly unique, instead of just removing them like it has been done.