Kevin - honest question - did you watch "Star Trek: Discovery", particularly seasons 3-5? If you did, then the tech changes spurred by the jump to the 32nd century (personal transporters, programmable matter, etc.) shouldn't be a surprise. (Although you may be confusing the personal transporters - which are still range-limited - with Discovery's spore drive, which is decommissioned by the time ST:SA starts.)
As far as the "big bad" being pirates - it's more complicated than that. Again, later-season Disco fleshes this out, but here's the TL;dr:
- There was a catastrophic event called "the Burn" which caused all dilithium to go inert, and anything with an active warp core to go boom
- The Federation as we knew it largely fell apart, with many worlds (including Earth) going isolationist for their own protection
- Starfleet - what was left of it - largely went into hiding to lick its wounds
- Criminal elements, particularly those with access to FTL drives that weren't reliant on dilithium*, quickly rose to power and took control of former Federation territories
- Later-season Discovery shows the Federation pulling itself back together and getting back to business, but a number of rogue elements remain
* I had to qualify this because some ships - like Romulan vessels - use different energy sources to power their warp engines. The presumption was that these vessels, while not as numerous as ones equipped with traditional dilithium-powered engines, would have remained viable.
I watched the first two episodes, and while yeah, it has its cringy moments, I'm willing to give it a shot. It has a number of things working in its favor - Robert Picardo is back as the Doctor, for one - but most of all, it's optimistic, and we can use a little optimism right about now.