so heres an image of a village on a newly generated world.. there are 4 waystones in this village... default config.. no changes at all.

{
"worldgen": {
"generate_in_villages": true,
"village_waystone_weight": 5
},
"teleportation_cost": {
"cost_type": "level",
"cost_item": "minecraft:ender_pearl",
"base_cost": 1,
"cost_per_block_distance": 0.0,
"cost_multiplier_between_dimensions": 1.0
},
"discover_with_item": "none",
"take_amount_from_discover_item": 0,
"consume_infinite_knowledge_scroll_on_use": false,
"consume_local_void_on_use": true,
"free_local_void_teleport": true,
"store_waystone_data_on_sneak_break": true,
"can_owners_redeem_payments": false,
"waystone_block_hardness": 4.0,
"waystone_block_required_mining_level": 1,
"prevent_non_owners_from_breaking_waystone": false,
"can_players_toggle_global_mode": true,
"teleportation_cooldown": {
"cooldown_ticks_when_hurt": 0,
"cooldown_ticks_from_abyss_watcher": 0,
"cooldown_ticks_from_pocket_wormhole": 0,
"cooldown_ticks_from_local_void": 0,
"cooldown_ticks_from_waystone": 0
}
}

I changed the way village generation works. For now, lower the "village_waystone_weight" value, in the future I might make it more configurable if I have time. If you (or anyone else) have a good suggestion for a good default weight, feel free to comment.