Unless i've just done something wrong (in doing something right) Temples are working fine so far for me, but then again i only have one, in a fort with enough useless migrant specialties for me to not notice lack of productivity anyway.
The trick i've found is that each temple is set to a diety upon creation based on what your worshippers need as a majority, (name of said diety can't be viewed from the locations menu oddly enough, but i do remember setting it to the most relevant, i recommend attaching relevant names and reading up on your gods for guidance, unless some UI can be put in) then allocate a large space (excluding the first tile, i recommend two dwarves for every 1 floor space approximiately to give them room because they'll often flood the interior and performers will benefit from the open space as dwarves often like to stand outside the 'interior zone' i've observed in my tavern for interactions)
I've got a modest sized room/burial catacomb 10x10 with a little abstract design cluttering up the floor and dwarves just roll in and worship in thier inactivity given that there is enough floor room to accommodate the current worshipper count of the fort for the temples patron i find, any excess temple worshippers that dont believe in said god just clutter the room up but are drawn to it (bit like flypaper really) because specifically it is a meeting point, and without other places to go to (large or numerous meeting areas in public areas) they'll allocate themselves while inactive to fufill thier overdue pent desire to worship (You could give a open air outside tempoary temple/s a go) denying 'floorspace' in which to worship (unlike organised gatherings at the tavern).
Running off this, my theoretical solution would be to build reusable rooms (spare dorms/barracks or store space) and plan ahead for increasing population milestones in order to retire existing chapels, and set up new ones with constantly refreshed follower counts (in a little number next to the deity on the temple creation before it is locked in) until the traffic between areas gets to such a level that controlled populations aren't queueing up for the same space (I smell a job stacking issue myself akin to pots being reserved for use on jobs that haven't happened yet)
As a point of reference, compared to passive subactivities (green) that are not being engaged, purple active subactivities are actually happening within the proximity (can be observed directly in taverns when numerous dwarves engage to dance, thier activity will turn purple whilst they are dancing on the jobs screen, as does as even stronger evidence observers watching the dance from the 'exterior' area)
That's my idea of how these systems work, but i have been taking notes (I take good care of my dwarves, even if most of them are cheese making freeloaders) And i've never seen anybody pray to my knowledge, i thought they just passively worshipped to fufill thier need whilst (i will try encouraging equal distribution of worshippers across temples to see if it's a population thing, since at the moment my tavern has a controlled population and runs smoothly with a equal goblet - floorspace ratio) they were inactive, given they dont grumble a awful lot about it anyway and i rarely check.
As a quick idea soundboard to additionally resolve this, you can attach rooms to chapels if i reckon that to be right, perhaps dwarves need a piece of furniture or a study/dining room to space out functions in the chapel (im thinking stone throne pews in my mind as a alternative) thats secluded enough to cut away the traffic to the main temple though toady's mention by his thread initially discourages this thought but i will try it anyway.