But do note I'm actually looking for objective design flaws, not opinions here. For example, some may want to say "Caesar's Legion was a dumb idea, post-apocalyptic Romans..." That's not objective; some people actually think the premise, backstory and origin of the Legion makes sense.
But allow me to start off with three criticisms I have:
1) Come Fly With Me - Why the HELL is this quest a part of the "tutorial" to New Vegas? For a game that's about making morally grey, difficult decisions that matter, this quest sticks out like a sore thumb. Yknow, quests like Hard Luck Blues and The White Wash are objectively quite simple, and yet you care about them because you feel immersed, as if you're making a real tough decision that effects human lives. And then there's Come Fly With Me, which the player struggles to give a flying [censored] about, because the basic premise is helping a bunch of ghouls that aren't playing with a full deck of cards, made only extra painful thanks to it's sheer length and habit of saying "SURPRISE! Thought you were done? NOPE! Here have another step of the quest!"
I think something that sets New Vegas apart from other Bethesda games is that it gives you a reason to care. It pulls on your emotional chords while also challenging you logically, whereas Fallout 3 for example, you may have a quest like the Nuka Cola Quantum Challenge, the Wasteland Survival Guide or Blood Ties, which personally? I could care less about. Those quests just scream "goof" in the sense that they don't give you the impression that they matter, and that the world won't be better or worse off whether you do them or not.
In that sense, Come Fly With Me sticks out like a sore thumb, and it's quite difficult to roleplay through given that 99% of people would meet Jason Bright and think "yeah this guy's off his rocker" and not have any desire to help him. A quest like this existing within New Vegas is no biggie; a "goof" quest existing is fine. But when it's a central stop on the "tutorial" of New Vegas? And when it does such a horrible job of representing the tone of the game to come? Goodspring's quest is nice and simple for a 1st quest, Primm has some incredible symbolism in that Primm is basically just an abridged version of New Vegas altogether, but Come Fly With Me? Just completely out of place, and has NOOOOO reason to be part of the tutorial. You hear about people getting bored with Vegas before even reaching Vegas? I promise you this quest is guilty for a large percentage of those.
2) No Map Marker for major locations like the Lucky 38 - You decide you wanna load up Vegas real quick and test-run a weapon or mod or the like, and for that you need to swing by the Lucky 38 to pick up a weapon or a companion or the like. But you can't fast travel there. You gotta fast travel to Freeside's North Gate and walk through. Meanwhile, should you ever desire to, you can fast travel to the Abandoned Prospector Shack in the middle of [censored] nowhere, or to the Molerat Ranch right next to the New Vegas Medical Clinic.
Now I can see the argument for giving the Prospector Shack or the like map markers; it gives the player EXP for finding them, which is fun, and it gives them incentive to go towards what looks like a humble pile of junk and actually scope it out. But to give such locations map markers while simultaneously neglecting to give map markers to the NCR Embassy or the Lucky 38? Just what the hell...Likewise, there's several completely unmarked areas across the river from Cottonwood cove, complete with enemies and loot. Do people not explore those areas because they lack map markers? No, because sometimes walking the unbeaten path is interesting and rewarding.
3) Invisible Walls -Josh Sawyer answered and said the reason for invisible walls was more or less to prevent the player from reaching areas where the player would see beyond the scope of what was actually made, resulting in the player finding an ugly eyesore. But you really have to ask, given AALLL the infamy this one garnered: was it worth it? Should they have maybe just done some work to correct those eyesore areas instead?
Typically, these simply block off areas that are of no strategic importance or interest anyways, but sometimes they do have an effect on gameplay. The gates of Primm for example, or a couple of hills around Bitter Springs have invisible walls that CAN disrupt gameplay. While some may agree with Sawyer's reasoning, none can deny that this was definitely one of the more infamous design decisions of New Vegas.