What people here largely seem to fail to realise is that, in the end, The Witcher 2 was never about who sided with whom, it was about a larger scheme of things that Geralt had been completely unaware of up until the summit in Loc Muinne. Hence the unmet expectations where there should be none.
First off, the Nilfgaardian invasion acts as force majeure, rendering the "pro-state" decisions in TW2 completely irrelevant, as an independent Temeria would still be far from stable when the Nilfgaardians crossed the Yaruga, and thus an easy target (alternatively, its new ruler(s) could not realistically secure their newly acquired positions there in such a short timespan), as for the Upper Aedirn, the best they could reasonably hope for against the Redanian+Kaedveni or Nilfgaardian army is guerilla warfare Queen Meve style, especially since one of the pillars of their state (powerful sorceresses) had been no more by the end of TW2. In the new political reality, their idealistic cause was bound to be a lost one anyway, so why include them in TW3? Were they to make a cameo appearance, how could they have contributed to the story in an impactful way, given the very nature of their ideas? I just don't see an opportunity for that, whereas Roche and Taler following the Maravel Plan have found their way in, and justly so.
Next we have the witch hunt. While it may seem that another major decision to help Triss and expose Philippa and Sila prevents this calamity, it really only postpones the inevitable as the only two major monarchs left in the North (and since Henselt is killed either way, it leaves us with Radovid as our only option, and he is completely nuts) did not hold mages in very high regard and it would make all the sense for them to use half an excuse to crack down on mages, especially since there is no denying their role in the success of the Nilfgaardian onslaught. With pursuing other paths in TW2 you just make it all pretty straightforward, with no Council and Conclave to sugarcoat the bitter reality the adepts of magic and various other mutants had found themselves in in the North at the end of TW2 - or did you think that with Radovid and those gentlemen from the Order of the Flaming Rose it could have been any different? Besides, technically speaking, including a reality in TW3 in which for mages everything is safe and sound would've been the same as creating two different games, hence couldn't have been an option in the first place.
No matter what «important» choices you make in TW2, the plan preceding the Nilfgaardian invasion is largely successful (with 2-3 kings dead, their realms in turmoil and the northern mages compromised big time thanks to the Lodge's actions), and you can't help but feel played when talking to Letho, especially if you let Shillard play his little spectacle at the summit to the royal amusement. The game itself is but a prologue, it is only logical that the choices you make while playing it will matter very little. CDPR did not disregard your decisions, they simply took them for their real value on the bigger picture.
So, while you may weep and curse CDPR for forcing certain decisions on you, they all make total sense story- and canon-wise when you give it a good consideration.