I have over 1,000 hours in R2, so that should say to you that what follows is hopefully fair-minded and balanced.
#1 - The Release
There's no way to ignore it. It's probably one of the worst AAA releases in a very long. It seems like eons ago, but hopefully we all remember when open field battles had capture points. And when transports regularly glitched through the coast. And the generally unstable AI and pathing issues it would have (sometimes not even moving all its units into battle). Only around patch 4 or 5 did I start to regularly play the game, and prior to then, I mostly played custom battle. After patch 4 or 5, I plugged in the occasional mod and found the game acceptable, though it wouldn't be until almost a full year of patches that Emperor Edition would bring the game to a point where I'd view mods as not absolutely necessary. And only at that point did the game itself seem to be pretty much crash-free for me.
#2 - The Design
In retrospect, the design wasn't as flawed as I first thought. The mono-chrome unit cards actually grew on me, and the mono-chrome building cards were at least easy to discern building functions with. Really, after seeing what Attila is planning on doing with unit/building cards (as well as unit flags), I have to say, Rome 2 was actually pretty good. Less aesthetically pleasing with unit/building cards than Shogun 2, but a little easier to glance at and know what I was doing. Plus, I found the campaign map naval transport situation actually an improvement over Shogun 2: it makes much more sense to have every unit on a boat than Shogun 2's system where a single gunboat could escort/carry the entire army stack. That said, transports in tactical functions were preposterously overpowed. And 1 turn-per-year was a disastrous decision for the Grand Campaign (another problem rectified by mods and eventually partially solved by the Imperator Augustus Campaign). Lastly, Civil War was a horrendous mechanic at first, but eventually got fixed and made into something more like defecting generals/provinces were in Shogun 2.
#3 - The DLC
An absolutely mixed bag. Personally, I enjoy CiG and HatG, and sometimes still load them up. They have good maps, are shorter in duration, and generally added a good deal of content (factions/units etc.). CiG in particular was well-done, because the map was less road-happy and you actually had to move through rough terrain at times. On the opposite hand, Beasts of War was very poorly conceived (though it did get a few more units after-the-fact, which partially made up for it). And Wrath of Sparta is just a snooze-fest that really adds nothing but a new map. For faction packs, I have to say, the Black Seas Colonies was the best (a very good pack of mixed-roster factions), while many of the others were good to average (Balkan DLC was the most average, in that Illyrian units are just super-armored Greek units in some ways while the other two factions have decent rosters).
#4 - Battles/Tactical AI
Battles are always pretty subjective, but I found the battles to be not that much worse than Shogun 2. Yes, for a while there was an issue of units blobbing, and there is still the issue of true phalanx formations not being available to hoplites. But morale and unit balancing eventually came to feel pretty solid, and this fell into place before even some other elements. The two major issues were: siege and naval battles. Siege battles still don't work very well, though now the AI uses siege equipment instead of always dropping it. It doesn't use it too well, except for ladders, but it does use it in a spotty fashion. Sieges now are below-average but playable, though it took a while. Naval battle is still utterly awful, though. Glitches, poor design choices, poor unit balancing, etc. are an issue to some extent even now. But, the meat of these games - open field land battles - works pretty well, and the AI's ability to flank actually seemed better than usual.
#5 - Campaigns AI
A real, real problem area. Without mods, the AI seems to assemble armies haphazardly, and for unknown reasons tends to favor bottom-tier units despite having enough money in many cases to have much better troops. Moreover, the AI used Forced March stances for almost the whole first year in a way that made no sense and allowed ambushes easily by getting too close to my armies. Strangest of all, though, was the naval situation... fleets that loiter in areas of attrition for no apparent reason (as in, I'd see fleets of factions that aren't even at war with anyone parking their fleet in an attrition area for several turns in a row). Fleets that raid their own territorial waters. And armies garrisoning the port of a settlement rather than standing on land to garrison it (thus meaning they have to enter a defensive siege from the sea).
#6 - Agents
One area with almost no silver lining. Agents were too generic, capable of doing roughly the same exact things (stop armies, sabotage buildings, kill agents/generals) with only a unique ability or so each. Further, agent spam at one point was tremendous, making a single-settlement start a die-roll as to whether it would be playable or not based off of the luck of whether you'd get crucial buildings sabotaged or not prior to getting a second settlement. Agents still are largely un-fun, as I always use Champions to train troops, spies to poison armies, and rarely use dignitaries other than in spots where I want to change culture.
#7 - Army System
Another mixed bag. Army traditions were a good concept that was under-developed, with too few traditions to choose from with some factions having useless options (like a buff for sword infantry for a side with only Falx-units and spears for foot inf). Similarly, forcing a unit to be in an army wasn't exactly unrealistic, but capping the number of armies based off of the number of owned settlements is still unfun, and for a while was imbalanced (with only two armies available for the first 5 settlements or so prior to one of the mid-range patches). But a hidden joy: no more waiting-30-turns-for-a-new-general. While a lot of hate was sent the way of the Army System, and some of it deservedly so, I have to acknowledge that at least I always had a general for every army, with only super rare conditions (agent spam of assassinations in a single turn) leading to a spot where generals were in short supply.
#8 - Rosters
This was a problem area. Iceni, Rome, Macedon, Seulicids, Parthia, Egypt, and eventually Suebi all feel well-rounded enough. Most other factions feel at least a little lacking: Arverni get Oathsworn but lack more than a couple units in any category, Pontus is in the same boat but with Bronzeshield Pikes, Greek States in some cases lack acceptable melee units, Carthage lacks melee units (aside from mercs), nomadic tribes lack foot soldiers almost at all despite having to defend in sieges (an issue Attila looks to be fixing by not making nomadic types having to settle at all until they want to), and so on. Again, mods fixed this issue to a great degree (DeI, for one), but it was a massive let-down that even some vanilla sides (again, Arverni and, until a certain patch, Suebi) were thread-bare.
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My overall impression with R2 is that it is at this point a good game (but not fantastic), and was bailed out by mods and freebies for a while until it was (mostly) fixed. It still suffers from the worst naval combat since Empire, has annoying issues with army system mechanics and agents, and has sieges that are marginally worse than most Shogun 2 sieges (themselves not exactly a highlight of Shogun 2).
And my overall verdict is that, unlike Empire, I will probably not play R2 much after Attila comes out... Napoleon and Empire were both good games in their own rite, in a way, and both grew on me and offered different things despite one being sort of an improved version of the other in some areas. Yet R2, with its lacking politics, lacking diplomacy, and other issues, is making Attila to look more like a fixed game than a different version of it. Attila has won me over to even considering a pre-order from what I've seen and read (and the fact that this info is only appearing a month prior to release rather than numerous months out).
While R2 is a good game now, it took too long to get there and had too many mis-steps along the way (BoW DLC, design flaws, etc) to say it was as fun as most of the other TW games. I got my money's worth out of it, but it won't be something I look back on fondly, and will probably collect dust on my virtual library shelf as soon as Attila comes out. While I'm glad R2 got continued support/patching, on this one occasion I have to say I'm not all that thankful for it because it both broke mods too frequently as well as was what any responsible AAA company should have done anyways... if a product is blatantly unfinished, I shouldn't be expected to praise someone who fixes it if they were the one's who sold it in the first place. I reserve my praise and thanks, instead, to the modding community, which often could create marvelous fixes for free and was never obligated to do so.
And that's that.