So Fleets have been out for a while, and I've tried them and poked them. I liked them initially, but once the novelty wore off I began to have some issues.
=== Clumsiness ===
Let's say I have a goal to destroy a Data Center. In Classic, I could grab Raiders, Raid Starships, Raptors, or Vampire Claws or Space Planes, etc, exactly what I needed, send them over, and get the job done. Any that are lost are replaced automatically at home. This is fine.
With Fleets however, there are annoying limitations. If I send the unit out, it'll be disabled due to distance from the Flagship. So I send the Flagship alongside. But then, what if I have units like Tesla Corvettes, which are terrible at raiding and really don't want to come with? If I keep them at home and try to find something else to do, they'll be disabled and thus useless. If I bring them with, then I can lose so much more if/when the raid goes badly, and they're not adding much.
Another issue is unit combinations. I have used the example of Spiders and Agravic Pods before - Spiders slow things down, Agravics have a bonus against anything immune - a fairly simple, defensive combo, that I can happily send to where it's useful and needed. With Fleets however, they are stuck with a Flagship. If they aren't in the same Fleet, then I must group two Fleets together to do this one combination, dragging every other unit in them alongside, and likely making them unable to go be useful elsewhere.
Another example is of an AI planet that really likes Concussion Turrets. I look through my three Fleets, and find all of them have one unit type that would be useful here. I send them over...and disabled. In order to use these three, I bring all the Fleets together...and thus have Fleetballed. Again, all the units that aren't useful here, because the Concussions would murder them, are stuck sitting around.
Fleets being pre-divided does help in a way with controlling them around and knowing where everything is, but it is extremely annoying to then have this distance disable effect, which is constraining what I can actually do with my units, and has led to me Fleetballing anyway, despite the pre-division being to help with that.
=== Procedural and AI Ship Groups ===
Currently, Fleets can be complete mishmashes of unit types, which can lead to very strange and borderline useless Fleets, which I cannot divide up to give useful tasks, due to the above Disable effect. This essentially means you are completely at the mercy of RNG to be able to do meaningful things. You can even have units that are contradictory, such as Spiders, which slow things, and Snipers, which do more damage to fast things, and you can't separate them properly.
This ties into AI Ship Groups. Before, the AI had a basic Triangle (Vanguard, Raider, MLRS), and unlocked extra ships throughout the game. You could spot these, you could plan for them, acquire a new unit to deal with it, upgrade it or something else. Currently however, the AI is essentially an "Everything" type all the time. It can have anything on their planets, and attack you with anything.
Combine your Fleets being 100% random, and the AI being 100% random, and it is very difficult to have planning or strategy here with your Tech, or Fleet acquisitions. This has led to me simply upgrading the Techs which benefit whatever I have the most of, as that's the only real option. Everything else is ignored. My Fleet choices are also the same - build on whatever my best Tech is.
I have also noted on the forums the problem of Battlestations. As the AI can send anything, there is no decision to be made in what turrets I build - the only option is all of them, and again the only Tech choice is what affects the most stuff.
=== Permanence and Experience ===
Currently, I think everything that can be captured cannot be lost permanently. Fleets are merely crippled, and Zenith structures go to remains. The only structures you can lose are the Cryopods and Home Settlements, as well as the Home Station (though that loses the game of course). This essentially means there is little permanent damage that can be done to the player, beyond some AIP increases.
Hacking is a particularly poor source of permanence. With the removal of Design Backup Servers, and no Fabricators or Advanced Factories to Hack, there are less permanent effects to do to the AI with this, and I'd note it's a bit disappointing that an opponent entirely of machines is barely hackable - I think the Dyson Sphere alone has more. Hacking was a way to make something you could lose (i.e Fabricator) permanently available, but now everything essentially is already.
In addition to that, the player now gains permanent power increases, simply by fighting. This to me feels very at odds with the whole concept of the game, which is to be sneaky, pick targets worth paying the cost for, and try to not alarm the AI too much. Instead, I can bypass all of that by just fighting over and over. Bypassing planets is essentially giving up experience.
=== Economy and Territory ===
Economy is something as a result of the recent updates. Energy production for the player has increased dramatically, and with low mark units being discounted on both Energy and Metal as you increase Tech, and higher Marks not costing anything more, economic considerations have been lessened greatly.
By that, I mean things like capturing and holding territory, for additional energy collectors, metal harvesters, and things such as Zenith Power Generators and Matter Converters has become far less important. A single Economic Station produces around 75% of the Energy a ZPG does, for instance. This has resulted in me having the behaviour of capturing a planet for a Fleet, then abandoning it immediately after, because it's near worthless.
Before I could build Turrets there, entirely separately, but now trying to hold it requires Battlestations or Citadels, which would either weaken my Homeworld, or increasing AIP, and neither is worth it anymore.
=== End ===
It hurts a bit to say, and I really don't mean it in a harmful way, but I've grown to really dislike the things in the Fleet update. I originally really liked it, and completely supported it when the design document was shown to me, but over time after playing it...it's started to become a game that I don't want to play or work on. I seem to be in a tiny minority though...plenty of people like it.