I have absolutely no issues with FONV system. Plenty of warnings for not heading north, through signs and dialogues, and if you still did it you deserve what happens to you. You're also warned to not stray off the roads due to wildlife, even if you did go the intended route. And yet, if you know the game well enough after quite a few playthroughs, you're able to take certain shortcuts to get to New Vegas and obtain all upgrades before even reaching level 2 (ED-E as melee, lure fiends into NCR territory and strip them clean, obtain a few expensive items and sell them at DLC vendor with plenty cash - exploitative and minmaxing as hell, but kinda fun).
The system reminds me on how we did tabletop RPG back in the day. If game master had something prepared, warnings would flurish for straying too far off that plan, and we'd get severely punished if we did. The only thing I don't like about FONV is the inability to get away if you mess up. Enemies of all kinds (I'm okay with deathclaws and cazadores) charges you until you are dead, and usually impossible to get away (those bulls are okay though, they warn you not to get too close). That did not happen in tabletop times, where we could often talk our way out of extremely sticky situations.
Least sense is Oblivion - low level bandits patrolling the roads at low level is okay, scaling them up also kind of okay. But turning them into Minotaurs when you're scaled way up is just stupid, even if you're fast enough to ignore them and just rush through. I would rather have the bandits cease to exist, with some story based explanation (not safe anymore due to some hero, whatever) or some quest to finish them off once and for all.
Not too sure if possibilities should be locked out completely by area this way though. Obtain all required special parts that enables super mods for your weapon by either:
1) Fight through one high level area with same level opponents.
2) Fight through several low level areas with level+10 opponents.
Same with shortcuts. Wouldn't be intuitive to "know" about these in a FONV first few playthroughs. Maybe similar approaches in FO4 - "you can, but there is no way anyone would know".