Skyrim - changing the levelling system. Yeah, I get it, it's not as deep as the levelling systems used in past games. I have seen people express that opinion and it's somewhat correct. The problem is that the Morrowind/Oblivion system was obtuse and obsolete to begin with. The "depth" provided was false and it just meant micromanagement of stuff you really shouldn't care about. Pretty much the whole crux of the old system was flawed. I truly don't understand how people are not OK with the idea of changing the levelling system considering that by far the most popular mods for both previous games dealt with the levelling system. And of them, by far the most popular were the ones that did changes similar to what Skyrim does - you just use skills and that increases your level and attributes automatically. Skyrim axed attributes altogether in favour of "do you want more health, magicka or stamina" and that's actually a step above. The levelling system mods had to work with attributes in place but those were redundant as well.
XCOM 2 - removing the air game. I didn't really like that from Enemy Unknown, removing it altogether seems fine by me.
Heroes 6 - a lot of it.
- buy your population from anywhere - I love, love, love the series but when I look back, I realise just how much time I've spent collecting my troops. In Heroes 3 the god strat was to have both the Wisdom skill, so you can learn Town Portal and the Earth Magic skill, so you can actually choose your destination. Thus you finally solved your population collection issue. But it was still boring. Go around, purchase all the troops, repeat - on large maps it became tedious. Just being able to buy all troops from everywhere makes more sense.
- removing some resources - if you're not familiar, the series has ran on the following resources: wood, ore, mercury, crystals, gems, sulphur and gold. For pretty much all intents and purposes wood and ore are the same thing - they have the EXACT same exchange rate with everything else and for the most part a building will need equal measures of both. Occasionally you get something that needs lots of one but not the other but whatever. As for the rest, mercury, crystals, gems and sulphur are in the same boat, although they do have a higher exchange rate than wood and ore. Well, also buildings do want exclusively one most of the time. At any rate, you essentially have three tiers of resources - gold, a common resource (wood and ore), and precious resources (the rest). Heroes 6 did stripped down precious resources to a single one: blood crystals. As interesting is to be strapped for those 3 mercury you need to build something, it's also incredibly frustrating. In most cases, each race has a high demand for one of the precious resources, so if you cannot secure income for it (entirely possible on random maps), you are in a bad place.
- removing random skill selection for a skill based system - if you've ever played the series enough, you'd have had a level up when the choices you have simply suck. It's super annoying when that happens. In general, you don't have a good ability to plan out your heroes, either - some skills are more likely for some classes, but other than that, you cannot really guarantee you'll get any. That's why that Wisdom/Earth Magic combo is strong - you could easily just not be able to get it. Heroes 6 instead gives you skill points on level up and you can just buy whatever skills you want in the skill trees.
- you no longer gain spells from the magic guilds - it's now actually a skill you buy with skill points. Again, the reasoning for why I like it is similar to the skills themselves - the spells you get are random and you can definitely just not have Town Portal at all. Even if you take over another town, you are not guaranteed to get useful spells, since you can get duplicates. And I can't express just how disappointed I've been when I get Summon Boat or Scuttle Boat on a map that doesn't have any water in H3. There is a good selection of spells that aren't really useful to begin with. At least with skills you have SOME control of what you get, with spells you really only need a handful but you could keep getting the rest without much you can do about it aside from keep rolling dice building magic guilds.