I mostly agree with you. Quake II was a decent game, but it didn't leave a lasting impression. The original quake was the last single player Id game that mattered.
I think Id was able to recreate the magic for Q3A though. When it released it wasn't considered phenomenal, but now that I look back over the years, it is one of the top 3 shooters of all time.
I think Id could be great again if they got together with some of the designers from fallout or the elder scrolls. Some cross training would be beneficial to both parties. The character animation in Bethesda's games are terrible; Id software can't write a decent story.