Honestly, I think there is an overarching problem with the concept of "Fleet Training".
Taking things literally: you mean to tell me that if I have my ships sit under a training HQ in Earth orbit for a couple of years, they will be 100% capable of being dropped into any fleet in the empire and having instant reaction time working with brand-new comrades (which is really the main, possibly only? thing that fleet training actually affects; I think everything else is Crew Training which is far more sensible), but if I put a fleet together and send them on a two-year patrol of the outer rim they will only have, what, 40% despite having worked together closely for two years? I think this strains belief as a game mechanic.
Meanwhile the actual mechanic is entirely micromanagement: shuffle ships between admin HQs, give refuel and overhaul orders, babysit to make sure nothing runs out of MSP, etc. etc. It's not interesting, frankly. VB6 was not much better mechanically, although less annoying due to "tricks" like using a slow ship in the fleet to reduce fuel consumption, but otherwise a pretty similar mechanic aside from the ships actually flying around (I do like how the VB6 reaction mechanic included responding to orders, though, not just fire control delays - much more realistic IMO though I can see why maybe it was removed for being too much).
I'd rather see "Fleet Training" removed entirely and more importance placed on the commander Reaction skill, which to be honest feels a bit marginalized since it basically is only needed to make up for a lack of Fleet Training (order of movement rarely matters in practice, and even less so in 2.0 with 1-second subpulses). More emphasis on commanders (excellent storytelling) and less on boring, micromanagement mechanics (poor storytelling) is a good thing IMO. I would like to keep the Training Admin HQ but as providing a bonus to crew training rather than fleet training, as these would still have a place in the hierarchy alongside NAV and PTL admins.