The problem is that the Borg are shown to have been assimilating species for centuries before they arrive in the Alpha Quadrant and there's no indication the process changed. I think you just have to consider it early episode wonkiness.
There's no indication of what the process
was in the first place. Which leaves us either dismissing the early portrayal of the Borg as 'wrong' and the
Voyager portrayal as 'right,' or assuming that at least a few things actually changed.
Given that the portrayal of the Borg is widely regarded as having gone downhill in that timeframe, I'm not sure I want to dismiss the Borg's "best" appearances as somehow 'wrong.'
Only flaw with that would be the Borg's lack of an assimilation beam.
Although, it's possible that the control mechanism used to tame the Beast is just too bulky to fit in a particle beam.
Plus,
unlike the Biophage, the Borg don't want to assimilate ships and installations by melting them into goo and using the biomass as control systems for the machinery. That's never been their modus operandi; if it was, they'd just build giant supercomputers instead of having their hive mind consist of billions of individual mind-linked drones. "Assimilation" would consist of uploading onto their server farms.
For whatever reason, the Borg actually have a deep rooted belief that there's something important about having specific individuals with recognizable bodies, all of whom are linked together to form the Collective. So while they can make use of the Biophage's ability to rapidly alter physiology, they can't just toss a blob of nanites at a spaceship and take it over in that way. They probably COULD use their assimilation nanites as some sort of 'biological weapon' even in canon, but they generally don't do that aboard ship.
Maybe they're worried about the nanites behaving in unpredicted or uncontrolled ways if they're applied to anything other than specific human(oid) hosts under observation by another drone? That would tie into your speculations about control.
I think the change would be a matter of when and how species were assimilated. Beast derived nanoprobes make assimilation much more efficient, so it gets applied more frequently.
I still prefer the idea of a nightmare Borg/Beast hybrid devouring all it sees.
My entire notion is that this is
exactly what we had to deal with already. 
Then again, maybe it's because I worry that the Flanderization of the Borg in
Voyager subverts our perception that they're scary, especially in a game where the Biophage exists as an alternative. The idea that the Borg are what they are because they encountered the Biophage
and ate it tends to heighten that in my mind, and re-establishes them as dangerous antagonists.
@OneirosTheWriter, I have to ask: No foreign analysis of minor powers, such as the Sydraxi and the Lecarre? The Syndicate, maybe? (The latter two would presumably focus less on ship-to-ship combat and more on countering infiltrators.)
The big problem with having techs for that is that those opponents may cease to be a threat within 10-20 years, making them less likely to matter. We know the Cardassians are going to be around for a while, we don't know if we'll still be fighting the Sydraxians in ten years' time.
