There's been longstanding arguments about Jellico, and whether Riker was "wrong" in resisting Jellico's intentions in TNG's "Chain of Command." I wonder if anyone has changed their position after Prodigy? Especially since he's shown to be wrong at almost every instance.
I think a pretty good argument can be made for why Prodigy shows his philosophy is wrong for Starfleet and the Federation, and lead to Picard publicly declaring "it was no longer Starfleet" in Picard season 1.
Jellico basically neuters the historical mission of Starfleet, and goes along with a societal change that turns the Federation inward. Instead of pushing outward, Starfleet becomes militaristic and basically repurposed to be a patrolling military force not concerned with the expansion of science and knowledge.
The synth attack on Mars becomes a 9/11-type event where it's used for a recomplete reordering of Federation society (e,g.., why would you shut down Starfleet Academy when you have a shortage?).
I think the issue between Jellico and Riker is entirely separate from the Mars attack issue. With regards to Riker, I would say Jellico was generally right that the crew had to adapt to him, except that his idea to completely change the ship's organisation, days before a confrontation with the Cardassian fleet, was madness.
But in Prodigy, I don't think he has always been shown to be wrong. His orders to destroy the Protostar in s1 were actually a good call, it would have avoided the major loss of Starships later. His order to not enter the timey-wimey wormhole because it was too dangerous: actually correct as well. As it happened with Dal and Majel, they nearly got the entire universe destroyed. In anothe reality where Janeway went herself, she got killed along with her key officers. Good call from Jellico.
Jellico recalled Voyager-A and the Protostar: probably a good call with the information he has, at least both Janeway's officers and the Protogies themselves agreed with it at the time. The headquarters and Daystrom etc. should have even more brains and info to throw at the problem, after all.
Telling Janeway Starfleet can't help them: just a statement of fact. In grand Starfleet tradition, the hero ships are the only "in the quadrant" and they also happen to have much faster drives than 99,999% of the rest of the fleet.
And the lack of starfleet vessels, along with the third major attack by the Vau N'akat within a year or so, shows that he has a point that Starfleet is overstretched, taking into account the massive loss of vessels and personnel at Mars and all the previous losses starting with Wolf-359 and the Dominion War. And even after defeating the Borg and the Dominion, it's basically still open season on the Federation and Starfleet (considering Mars was a Romulan attack - which Jellico and his fellow admirals may well suspect).
Moreover, Jellico is the "spokesperson" for Starfleet Command in Prodigy but he is not sole ruler of Starfleet and/or the Federation, obviously. He is merely Janeway's direct superior, probably in charge of a certain fleet/area or at most of Starfleet Operations in general. He does not make those calls alone, may not even agree with some of them.
He especially shouldn't be involved with Starfleet Academy. The decision to close it for the time being, which is indeed a very weird decision considering they need to be training new personnel pronto, can't be his alone and he may not even have been involved (not his area of responsibility).
I'm guessing that Starfleet Academy, in its present form, is seen as taking too long to train new recruits (and to have too high standards) and it is being replaced by "on-the-job training" (as the Protogies have been getting and will continue to get with holo-Janeway) and by more limited but more numerous training courses planetside. Some of the instructors may be recalled to active duty in Starfleet installations.
Basically, I think Starfleet is conforming to the new reality and setting defendable priorities. They are the only form of defense that much of the Federation (including Earth and such places as Betazed) have.
They made out like Jellico was the boss, but I don't see how one person could unilaterally do all that. He may have led the charge, but plenty of Badmirals had to have been onboard.
My issue is that I don't see how Strfleet ended up so completely understaffed following the Dominion War. Wars often lead to periods of rebuilding and expansion.
Agreed on Jellico not being the boss of all of Starfleet, but I don't think those others deserve the label "badmiral".
Starfleet had enormous casualties during the Dominion war, and now again at Mars, and in between some minor disasters. They were already stretched thin during Prodigy S1, which is why Berniss Frex was alone in his relay station.
Also, it is said that Jellico militarises Starfleet but then Starfleet is the de-facto military arm of the Federation (with the possible exception of Andorian and Vulcan fleets, who may retain military value, there does not appear to be any other form of defense but Starfleet). One could level the same complaint at Sisko (build the Defiant - a *gasp* warship and it cloaks - and then militarized the Federation against the Dominion, together with "badmiral" Ross and with illicit help of a Cardassian agent) and at Janeway herself. Note how Janeway, in her incomparable style, embarked on her own war with an entire enemy planet and subdued it by herself in a matter of days (or a couple weeks at most). How many Vau N'akat vessels did she destroy? Oh, and she also illegally used cloak - multiple times - send agents undercover to undermine an alien society - and broke numerous treaties.
I don't think the admiralty can just plan to always have one or two vessels miraculously defeat large enemy armadas that would normally be able to annihilate entire fleets of Starfleet vessels. They need to focus resources to both keep the Federation running (replacing the now defunct androids in some manner) and to defend it.
