Hey @Stu, your idea in that GURPS (YEAH!!!) game to clap your hands and listen for the echo to determine the depth of a well is actually quite simple. Sound travels through air at about 340 meters per second, so you just clap your hands and count the seconds until you hear the echo, then divide that number by 2 then multiply that by 340 for an approximation of the depth. (The dividing by 2 part is to take into account the fact that the sound wave has to go down then back up, so it covers twice the actual distance you're trying to measure.)
So, in short, your GM that didn't allow you to do that was an ignorant dick!!! Or just ignorant, but that's a more boring conclusion.
As for the issue of the player-vs-PC intelligence gap, I kinda liked Option 4: let the smart player come up with the solution and "give" it to the player of the smart character. A broader approach to this could be to let the players solve the puzzle together (thus giving the players the fun of solving an actual puzzle) but then maybe everyone rolls an Intelligence check for their characters, and whoever has the best roll gets to be the character who solved the puzzle in-game. That way the smartest character will be far more likely to solve puzzles in-game, but all the players still have the fun of working on them together, which simultaneously simulates the super high intelligence of a much smarter character.