I tend to think of certain specific scenes from the old Clone Wars shorts as having happened more of less as depicted (Anakin's knighting ceremony, swapping droids with Padme, Ventress's intro etc.) rather than the larger narrative.
Yeah, a lot of the details are iffy, both from a continuity standpoint and a plausibility standpoint -- not just stuff like Mace's Force-wielding being absurdly powerful, but stuff like droids and clones jousting on speeder bikes. Not to mention how different many of the character voices and accents were. But a lot of it might still work in broad strokes, and a lot of individual scenes could still work -- for instance, the scene of Dooku training Grievous in lightsaber combat foreshadows Grievous's line from ROTS, and if that training came as late in the war as shown, it would explain why Grievous only mentioned it during the final battle on Utapau instead of during his many earlier fights with Obi-Wan in TCW.
I used to think they you could indeed slot TCW pretty much into the second season's opening montage, but the Siege of Mandalore pretty much put paid to that idea, but if I'm honest I'd *much* rather have the Siege of Mandalore story, so no huge loss.
Oh -- I have the novel
Ahsoka sitting on my read pile, but I haven't started it yet (though I plan to do so tonight or tomorrow). So I didn't know about the Siege. From what I see on Wookieepedia (skimming so as not to spoil too much from the novel), I take it that it leads directly into ROTS?
Anyway, I think you mean the third season's montage, since the whole Muunilinst/Ventress arc spans the first two seasons of ten 3-minute episodes each. The first season ended on the cliffhanger of Anakin chasing Ventress's fighter into hyperspace. (Which, by the way, seems to be a continuity error; in one of these threads, we were just discussing that there normally doesn't seem to be a way to pursue a ship directly through hyperspace, but here, both Anakin and the clones on the ground were somehow able to determine the fighter's jump coordinates before it left.)
The third season begins with the resolution of the Grievous cliffhanger from the end of season 2, with the Jedi finding Ki-Adi-Mundi and the badly injured Aayla and Shaak-Ti as the only survivors of Grievous's debut attack. It then moves into Anakin's graduation from Padawan to Knight. It's episode 2 of the season (22 in all) that opens with a time-jump montage to the latter days of the war. The 3D series would have to be within that montage -- though not before it, since there's a scene where Padme reacts to Anakin's newly obtained facial scar, and I think he had that feature throughout TCW.
I do wonder if TCW consciously avoided retreading the same territory, at least in the early days if only to keep a respectful distance. There's a mention at one point in TCW of Mace being embattled on Dantooine, which is a clear nod to the micro-series.
I figured that was why they treated Ventress and Grievous as pre-established characters, instead of giving them new debut episodes.