Fortunately, Mike Mearls has told us a little bit about the process. I'm not going to spend an hour and a half attempting to find the articles and quotes
They've all been taken down, anyway...
When determining what to include, they look at how popular something is, but they also look at how unpopular it is.
Not anything I ever recall them saying leading up to or during the playtest. The emphasis was on making a D&D for everyone who every loved D&D, not a D&D inoffensive to D&D's loudest detractors. Cutting things that a sub-set of people wanted to deprive others of is no way to create an inclusive environment.
If anything, in 'The Gnome Effect,' Mearls outlined the opposite philosophy: that if even 10% of players might be disappointed by lack of an options, that'd statistically impact about half of 5-player tables.
With those, most people said the Runecaster worked fairly well, but a lot of those same people (I believe it was either 40% or 60% of all respondents to the survey) said they do not want prestige classes in the game (including the Runecaster).
And this is just nonsense, given 5e's modular approach. I may hate spellpoints, I might have nothing to do with a D&D that enshrines them in the core rules and makes them difficult to extract, but, there's a system like that in the DMG, and I'm free to just ignore it. 5e is meant to be customizable and adaptable to any style or 'creative agenda' - it is not meant to validate one preference over others, even if it is the largest preference according to this survey or that vocal segment of the community.
I suspect this is exactly what came about with "Damage On A Miss". Same thing might be with Prestige Classes as you say. At some point, if the disdain is really that strong... you're just better off going back to the drawing board to come up with something better than to continue down a path that enough people already hate.
It could also explain why the warlord didn't make it either.
Or Psionics, I suppose.
But, I suspect a lot of considerations when into cutting things with as much potential as PrCs or the Warlord (or any non-DPR-focused martial sub-class, for that matter). One of the big ones that Mr Mearls went back to over and over again throughout the playtest, though, was 'classic feel.' Another had to be the difficulty of actually developing content. D&D doesn't have the kind of development resources it used to. If a particularly project gave him trouble (and he expressed having difficulty with the Fighter, Warlord, Sorcerer, and Ranger at various times), he couldn't just delegate it to a team of 10 for extensive playtesting & re-design. A genuinely versatile/interesting (thus highly complex) martial option, whether literally a fighter (which would have meant putting even /more/ of the class into the sub-classes) or an actual Warlord would have been both difficult to design, and would have to have been entirely novel, since it couldn't just leverage a lot of existing spells, for instance. Building on the playtest Sorcerer would have been a lot more work than just creating a somewhat different casting mechanic, re-tooling metamagic, and picking a new spell list from those of other classes (literally, the Sorcerer is the only caster with no spell at all unique to itself).
Anyway, just some speculative alternatives to the lowest-common-denominator theory of cutting potentially great stuff from 5e.
DO NOT! use that word round here.
The Temporary Warlord Forum has been folded back into the 5e board.
What word? 'Warlord'? We shouldn't use 'Warlord' around here? Okay! Sounds good! No using the word 'Warlord' around here! You hear that, everyone? No using 'Warlord'! 'Warlord' is verboten! If we hear anyone using the word 'Warlord', there will be hell to pay!
Though, of course, Morrus could always bring the Warlord Discussion Ghetto back....
