I just finished running a 3.5 conversion of G1-2-3 and D1-2-3 last Monday, so the OP is near and dear to my heart at the moment.
I love the modules, but they are better viewed and run as a campaign setting than as modules. And while the individual components are fantastic, the narrative thread that hangs these pieces together is fundamentally a pretty weak one. (And originally, the modules were designed separately for tournament play, so a coherent connective narrative wasn't that important.)
Sure, because the drow are super chaotic and super evil, and because there are plenty of other evil races down there in the underworld, one can hand-wave any number of illogical plot twists by claiming it is all "an intentional part of a devious master plan" or "an error stemming from the dark elves' innate chaotic nature."
But that still doesn't help that most games will begin D1 with the PCs intent on finding and destroying Eclavdra and her minions. And because the PCs are entering an extremely hostile, alien environment swarming with an intelligent, numerous, and powerful enemy, they should be trying to move as quickly and quietly as possible on their way to the Vault. Which means not only CAN they bypass the Shrine of the Kuo-Toa, they SHOULD try to bypass it.
And for that matter, the warrens of the troglodytes and the whole Vault beyond the Black Tower, Erelei-Cinlu, and the Nobles Plateau should also be avoided if the PCs are playing intelligently. That's probably 80% of the D series.
To put it another way, the structure of much of D1-2-3 -- site-based exploration -- is completely at odds with the framing narrative of infiltrate and destroy. A DM determined to have his players see "all the good parts" will need to introduce numerous extra plot hooks (or else ignore or radically alter the framing narrative) in order to entice players off the path. And even then, I think most intelligent players would be loath to forget the mission.
I believe Gary himself has reported that in his original playtest, his own players avoided most of the encounters and only peaked around the Vault before beating feet. So this certainly isn't a new problem with these adventures.
True to form, my own players avoided most of the warrens and the shrine. I was preparing for an assault on the Temple of the Elder Elemental God, but I also had Eclavdra herself approach the PCs with an offer of truce. She argued that, by destroying her giant scheme, the PCs has greatly weakened her once-great house, which was the only significant source of opposition to the Temple of Lolth. Destroy the Eilservs, she argued, and the Temple of Lolth would be strong enough to directly assault the surface world, which was still reeling from the giant attacks. And besides, the Fane was said to hold many great treasures and much magic.
So my players agreed, and infiltrated the Fane using veil spells (Eclavdra helpfully provided some intelligence on the layout and defenses.) The PCs slew High Priestess Charinidia, assumed her form, and then ordered the Temple and all its allied houses to launch an all-out assault on the rebellious house Eilserv. (My players really enjoyed playing political games with the various drow factions, and I thought this was a most worthy double-cross.)
The PCs then found the secret wharf cavern (Eclavdra told them they could use it as an escape route) and stole one of the ships, and are now making for the Sunless Sea with great haste while the Vault errupts in bloody civil war. Mission accomplished.
