That sounds like yet ANOTHER way that C3C makes the game much easier to win (in addition to that new corruption model with the super-scientists). I'm not a fan of making the game easier. I'd rather work with the challenges.
I don't think that it is easier to win with Conquests than PTW. (I've not played vanilla.) The challenges are just different. For the way I like to play, Conquests is more fun, though. Because of GOTM/COTM, I play both a lot, and I win comfortably at emperor, usually at demigod, occasionally at deity, not at Sid. My preferred victory condition is 20K.
Combat settlers can be a part of either game. When taken to extremes, you can penetrate very deeply into enemy territory. What you do is build a town, move a settler one tile past the town, abandon the first town, and settle again. If you want to have a continuous clear path, you will need to resettle behind as you go, too. With enough settlers you can go all the way through enemy territory. (Note: I have not done this myself, as I am too lazy to build zillions of settlers.)
The new corruption model makes Conquests harder - before Conquests you could use the remote palace exploit or RCP to dramatically reduce corruption. In PTW I count out distances before placing a city, in Conquests I don't. This makes Conquests more fun, but more difficult to win. Better specialists allow your corrupt cities to be more useful in Conquests, but you have _many_ more productive cities in PTW, especially if you place your cities and FP carefully. I would say, Conquests is easier to play because of the corruption model, but PTW is easier to win because if you place your cities carefully the payoff is huge.
In PTW, military GL are really nice. You can get lots of them if you spend lots of time leader-fishing or playing always war. I don't like to do this. In Conquests, MGL are much less useful, despite the nice armies. Instead SGL rush wonders (except in COTM, where they are turned off). You get far fewer of them, but you get them by fast research, which I like. I think the wonder/army issue balances out about the same in terms of difficulty, but the choices are different in the two games.
The new bombardment rules do make Conquests easier. Artillery units attacking cities attack units first, rather than a random selection between units, buildings, and population, and this makes taking a city a lot easier. Lethal bombardment is also nice.
I think the changes in civ traits about balance out, unless you select your opponents to give yourself a big advantage - playing Sumeria (agricultural and scientific) on a no-hut map with all expansionist opponents, for example.
Faster forest chopping is balanced by volcano pollution.
I like the 100K cutoff change with mapsize, but it doesn't affect the difficulty of the game.
For modern warfare, the addition of some units and upgrades might make Conquests more interesting. If your opponent get to the modern age, it makes it more difficult to win because the TOW Infantry require no resources to build. In PTW, if you can cut off an enemies resources you'll be facing defense 6 units. In Conquests they will be defense 14; a cavalry army can usually take out a redlined TOW in a city, but not a 2hp one.