Honestly I think my favorite mod overall has been Fallout Doomsday (for DH, lol. I played HOI2 DD way back in the day but never found the modding scene since it was a copy from a friend.)
It has been a long time since I last played, before many of the updates that have since been made to that mod (pre white walkers and nukacola and whatnot) but back when I did it felt like the most polished and complete mod. Even Kaiserreich is full of dramatic lapses in quality and dead end countries. Historical mods I have mostly shyed away from due to the railroading inherent to most of their designs, and poor balance decisions such as the forced insertion of unique/elite units.
Number two would be KR 1.8 or so, which I modded heavily for my own uses as I find is sadly necessary with that mod. Generally I think the problem with old mods or rebuilt mods using another as a base is there is a dramatic drop in quality that seems prevalent as of late. People ignore the existing graphical norms (including color or sepia pictures in a mod with all B/W imagery, different flag styles..), or totally ignore any sort of polishing to that end (no white borders on their leader/minister/tt icons, poor resizing..)
Something I also hate but which seems very prevalent is an increasing lack of choice and randomness, with events popping up that seem to tell the story of some whole crisis or political machination as if it just happened and you're just there to witness it, no choice involved. Or a coup that fires which is unavoidable, or some series of events beyond the players control dictating a certain outcome.
One of the things that pissed me off with KR 1.8 or so was the new development team seemed hell-bound, probably for some sort of reddit-tier personal political reasons, to have Goering removed from Mittelafrika no matter what the player's choice, with the addition of new events for GER that gave him something like an 85-75% chance of removal constantly every year until the war in Europe starts. And then despite that, after all these years, the ACW is still a huge mess, and the CSA and AUS and even USA have stupid, shallow event trees that go absolutely nowhere, and are sometimes even quite broken. Very simply QOL fixes are somehow ignored in favor of fixing things that are not broken in China or South Africa (which now undergoes an utterly pointless civil war over apartheid of all things, which was very clearly written out by a very biased developer. A shame since I used to enjoy playing SAF beforehand, as it was a country with many gameplay choices, if few events.)
Certainly that's why I could never say KR is my favorite, since in my opinion it's only really a good mod again if you put something like 20 hours into modding and testing it yourself.
FODD on the other hand you at least used to be able to play as the devs intended for the entire game with little issue, even if there were a few balance problems like the Spiders steamrolling everyone or the Enclave being a pushover.
Thunder in the Sky is another good mod by a veteran modder here, but it suffers from some wild inconsistencies given that it includes a lot of (now very dated HOI2 era) MDS material for TTs and leaders of many countries. Another issue is it also feels very railroaded at times and there is rarely much choice offered by events, even if it has many of them.
Fatherland is a similar mod which focuses very heavily on combat, but I think suffers due to huge army buildup from the very beginning of the game and therefore also allows ultimately little choice.
Bonaparte's Legacy is an intriguing mod which is plagued by a legacy of glitches that prevented me from really playing much of it, and which I have not touched again in at least a year or two.
I just realized how rambling and disorganized my post has become. Here is a list as you wanted.
1. Fallout Doomsday (at least, how it used to be. Have not played the most recent versions.)
Positives: Entirely new and very appealing graphic style based on the old Fallout 1 & 2 games, with a unique setup that allows a fun sandbox experience with all but one or two countries (USA is railroaded into a civil war, and a few countries are almost impossible to expand due to their positioning, mostly those in California, though there are no limits on your ability to make alliances or wars). Was a very polished mod that looked and played great.
Negatives: A few balance problems; used a centralized IC and resource system that means countries can very easily snowball, especially those for which manpower is not a huge factor, as one can easily double or tripple in IC by taking over and acquiring cores on conquered countries. I would have preferred most of the IC that nations have was provided offmap to reduce this snowball factor. Also suffers from some serious performance issues early/mid game when the wasteland is "on fire" with mutants and raiders. Map is relatively small (E3 USA map). Recent versions (Last played when the white walker faction was introduced, before nukacola) are much less graphically consistent and do not feel properly balanced.
2. Kaiserreich (have not played since 1.8, IMO REQUIRES individual modding ability to make fun)
Positives: Almost unmatched depth in a creative and inspired new world, which still offers some sense of sandbox even despite the masterful efforts to maintain some sense of interconnection and consequence to individual nations actions. In-game possibilities are almost endless and no two games are ever completely the same.
Negatives: Many areas are lacking polish, and many new additions are very poorly implemented. Graphical consistency in particular suffers immensely with many icons lacking white borders or not being grayscaled. Balance suffers from a strange DH Full / classic HOI2/DH hybrid model where units take a very long time to produce but do not utilize the DH Full mobilization system (thankfully, as that itself is a mess to balance.) Mobility Focus feels even more overpowered than usual, being an absolute no-brainer for most countries, and individual modding to preserve balance or improve new additions, especially on the graphical side, feels almost required for an enjoyable experience.
3. Thunder in the Sky
Positives: An interesting and unique world brought about by the results of a classic HOI2 AAR, with crisp look and performance due to relatively small armies. Offers a lot of promise with regard to both geopolitics and internal politics in much of the tripolar world. For the most part very well balanced, certainly better in terms of doctrines than KR, and very impressive considering it is mostly the work of a single man.
Negatives: Very shallow and at times choice-free event structure for what countries that have events, several graphical glitches due to image sizes and inconsistencies owing to the influence of two or three mods that were used in the development of this one. OOBs have several issues with missing attachments and a feeling of inescapable same-ness regarding army composition and starting models. Much of this is to be expected considering the heavily WIP nature of the mod. One issue that is inherent to the scenario design is the vast portion of the time spent playing the mod will be spent waiting for the two or three scripted wars to start over the course of several in-game decades. Nations are almost all hard-wired to build nothing but IC until 1985 and AI can be quite poor at times. A modifier.csv error in the live version at time of writing also makes combat logic somewhat crazy, especially in mountains.
