Manuals - I know you don't like doing them but you're the only one who knows everything about the mod (more or less,) and people who make various races need to do this as well: Keep up with them. make sure the manual documents everything major and even some of the minor. For example, the crucible in the manual didn't mention needing x number of boulders, nor do the relevant minerals. It was infuriating the first time I tried to process raw mithril when I had some and fuel only to realize I needed 3 mithril boulders to get anything. Chances are there's stuff I haven't done simply because the manual was less than helpful as to what was needed or what something did, or what would be a warning sign of what, exacerbated by issues concerning if it's clear in-game.
Diseases - You've heard me say this before. They need better documentation and/or a rewrite at the very least. The manual is no help other than 'it does this and spreads this fast' and a combat report tells me nothing about a disease unless it's super obvious, especially since several of them don't bother dwarves enough to make them see a doctor until it's practically killed them already or a chronic issue (stop complaining about your damned eyes Urist, they can't fix them!) I know someone else wrote them but at least some helpful information on what report goes with what disease in the manual under a spoiler would be nice. I'm also in favor of anything that can possibly cause permanent unconsciousness to just have that effect be replaced with "fatal stroke" instead. It saves a lot of trouble killing them yourself and keeps trade from being screwed up by that one jerk merchant who went and had a blood pressure spike in the caravan.
Alternative/other metals - Some people have complained about Bloodsteel and Ironbone, but I personally fine them as a great addition. It takes some pressure off hunting for metals when you can use other materials to make something just as good from renewable resources; it also lets you order other things from caravans instead of coal and ore. Like booze for example. On that note, the alchemy lab should probably have those reactions placed in a separate workshop that can be accessed without research; You already have to sacrifice food (do you want to be able to eat that meat or fend off that goblin with something other than a copper sword and no armor?) or buy blood for Bloodsteel and use bones you could have used for crafts or training ammo on ironbone. No need to shoot people in the foot by making them possibly waste effort researching the lab.
SOmeone complained about bifrost and volcanic (I'd be in favor of a different name for that if a better one can be concocted,) when you need to work to get those by either great resource investment or killing one of the toughest ivading forces, with thier effectiveness reflecting the effort/danger in much the same way Adamantine does with the risk of demonic incursion for harvesting it.
Standardized materials - I love it. While it is a little annoying to only get generic stuff from things like titans, it's less shit to make the game track and less to track = a better running game performance-wise
Races - I feel the hermit was a pointless addition. I mean it, I really do feel like you wasted your effort on that, not because it was a bad idea, but because it's not something a lot of people will play or want. Part of the fun of playing a hermit fort is watching the migrants show up and die because they eventually start killing each other due to lack of beds, clothes, or what have you.
Succubi felt a little... Forced, to be included. They really don't feel like they fit well like the Warlocks did. Boltgun did a great job on them from the looks of things, but overall I feel like they shouldn't have been included in Masterwork and would have worked better as their own expansion to vanilla. Kind of on the fence about the Drow as well because they kind of feel out of place in DF in general, but I'm used to them in Masterwork as an unplayable enemy/ally and if they stayed that way it'd be fine. They're a race that I feel really shouldn't be made playable for Masterwork.
Carp God - For the longest time carp were feared and rightly so. I find them a fun little threat to have as it stands to reason some would start to worship those fell fish in hopes of appeasing thier violent dorf-eating nature. I don't know why anyone would have complained about them, or the secret fun in general since it can be disabled before worldgen. Hell, I've never even run into them.
Dwarven Religious System: Dislike the references to armok, both in buildings and the wards. Shrines, Wards, and Temples should just be shrines, wards, and temples, while the Oracle of Armok can be changed to just "Volcanic Oracle." That way it feels less "meta" as it comes off instead as your dorfs call upon your civ's pantheon rather than an entity that they actually shouldn't know about. Plus on that last one dwarves often have volcano gods anyway so that's a win win.
Magic for Dwarves: I like it. They get a pinch of evil and good magic with things they'd regularly work with, as well as being able to act as considerably more versatile (or niche depending on your outlook,) troops at a great cost in resources (both in getting the alters and upgrading mages, especially in large numbers.) Need some heavy hitters for crowd control? Earth School. Web flinging FB? Air School. Firebreather? Sick the Fire School Mages on it. Want to hold an enemy at a bridge over a body of water or have to fight them near a crapload of ponds? The water mages can fight there safely (for a certain value of the word safely.) They fill various roles that regular dwarves can't and traps may take too long to prepare.
Trade nerf for dwarves: I read somewhere that the dwarves can't sell things anymore, which I find kind of a bad design choice. Long before the humans were playable the dwarves were able to buy and sell what they wanted in exchange for a trade license to build the shop; made it a great way to get rid of excess materials and get fewer, nicer things, or things you needed in a pinch. Or wanted to be rid of that copious mountain of leather you'll never use to pay for those relics that may or may not result in monsters killing everyone in the fort.
Excess workshops: I can agree with this to an extent. It does feel like there's way too many needed to get the most out of things, like the ore processor and the whole "need to process ore thing or only get a little metal;" it's just an extra workshop and step for the same result and would probably be better made part of the harder smithing option rather than default at the least.