EDIT: For the people slinging insults, I knew there was a problem with the FO3 and Oblivion quest tracking system, but I never associated it with the context of hurting the experience of exploration. It is not as though I thought everything was perfect before I read the thread.
I ultimately realized that Oblivion, FO3, and FNV are horrible "exploration/sandbox" games due to the inclusion of those features. I get a "tunnel vision" effect when I see those glowing beacons and like a moth to a flame I forgo all else and blindly race toward the next "flagpole" instead of investigating and exploring. Fallout 1 & 2 did a much better job of this by giving lots of clues as to where I should go without grabbing my hand and pulling me along. It takes a bit of acclimation to become used to actually investigating and exploring, but for the people who get over the initial system shock the experience is more rewarding beyond measure.
EDIT: Yes, FO 1&2 required a lot of investigation, but it was not super hard to figure things out, especially for the main quest (multiple NPCs in every location gave hints on where to go next). There was no real mandate saying you had to do anything other than explore (FO1 did have that darn time limit for the water chip, but that was far from the end of the game. It was up to the player to decide where to "explore" for new clues... kind of what you would want in a sandbox game right? In Oblivion and FO3 you were given specific locations... and you would NOT receive any helpful info if you decided to go anywhere but where the main quest dictated.
I guess the short of it is: I will not buy Skyrim until I find mods that remove the compass beacon and somehow turn the map markers into a vague area instead pinpoint precision. Please contribute to this discussion with ideas that add to or elaborate the arguments for or against these game features.
EDIT: The games are touted for their "free to roam/exploration" and yet they force feed you beacons on the compass. The compass markers for locations you have not yet discovered are another such feature that pulls my attention from exploring to "follow the marker". I have no problem with unexplored locations being put on my map when I get near them (not the explored/fast travel markers) like the way the "unexplored location" markers that you would receive after talking to people about places. Sort of like how daedric shrines, some forts, and caves were marked on the map. In FO 3 and NV the "unexplored location" markers would not be placed on the map if you wander near them yet the compass would have a beacon leading you there (pretty sure it was that way in Oblivion too). The map marker would give me a general idea of where I should explore next, but having to follow a compass beacon tends to lead toward following a specific path straight to the destination.
In short, I would much prefer unexplored locations being indicated on my map instead of using the compass beacon system used in Oblivion, FO3, and FNV. Again, the beacons will inflict "tunnel vision" on me at times and keep me from actually exploring.