I'm chiming in late to this thread, but what they hey.

I mainly agree with the OP.
I love the technology / game play / strictness changes with FNV. That is my number one love for the new game. I like the tighter skill points, I like the fewer perks, I like the changes to Speech and Repair, I like the companion wheel, I like hardcoe mode (tho I'm not sure I'd use it) and I really dig caravan.
Other than that, however, I give the nod to FO3.
I think most people agree that, in terms of exploration and dungeon running and world size, FO3 is bigger, better, and more sandboxy.
After that, dissent seems to come with quests and roleplaying and story.
I do feel that FNV is perhaps a bit better written.
Otherwise, though, I find both main quests equally un-interesting. I feel more of a personal tug from FO3, but both are largely un-interesting.
I also kinda feel the side quests in FNV are rather lack-luster, and dont have a lot of replay value. I mean, I like them fine, and there are more of them than in FO3, but I guess they don't motivate me much.
Also, my own personal inclinations make any depth to multiple endings in FNV more or less irrelevant. I have a lot of room in my brain for differences in personality in my character for different play-throughs, but still none of them could ever side with House or the Legion. So for me it just comes down to Yes-Man or NCR. Even then, I don't see going pro-NCR in terms of main endgame control. All the character concepts I'd play, from Vengeful Drifter to High Tech Brawler to Mean-Tempered Ornery Lucky Cowgirl, well they still would largely respond to most things the same way, because they ways in which they differ don't interact with the options presented. So most of them. given choice A, B, C or ignore, are always going to do A or ignore. Never B or C.
Also, even if I were the type to play a comic book evil character, just because a few of the choosing sides quests are different at the end, still the slide show is just faction A, B, C, or D won, with some side notes on how your Karma impacts it and on how other factions turned out.
But, I dunno, somehow, I just don't *care*. I'm interested to see most of whats out there on playthrough #1, but my second and third playthroughs (alternating between them) have been pretty much just about the builds.
Also about FNV having moral shades of Grey, I dunno. Powder Gangers are Evil. Legion are Evil. House is Evil. NCR citizens and soldiers are Good, but the leadership is corrupt. But when it comes down to individuals, they are basically Good. Perhaps that makes them "Grey" but not any more than, say, the USA. So that makes any moral "Grey" in the NCR feel mundane/typical. The Followers of the Apocalypse or whatever they are ... Good. Wacky but Good.
The only group I view as having an interesting morality or "in between" would be the Brotherhood of Steel. Helping people by protecting them from technology, all while making themselves more capable through said technology. Definitely a 2-sided sword there. I think whether that is more to the good or more to the bad comes down to Cult of Personalty and how the commander of a group decides to roll (as presented by FNV).
But generally, FNV morally grey? Nope. I see almost every faction as one way or the other.
So I guess in the end, I find FO3 more compelling, simply because the factions don't really interest me a whole lot in either, the side quests arent super compelling to me in FNV (even if there are more of them), the main quest is more or less equally uninteresting in both, but the FO3 one is a bit more personal to me than in FNV. The moral complexity, due to my own ethics, is roughly equivalent. This pretty much leaves it down to "feel of the setting", "exploration potential" and "game technology". Feel and Exploration go hands down to FO3. Game Tech goes moderately to FNV. All other issues (main quest, morality, side quests, game-ending options) are strictly a draw. This leaves me leaning to FO3 for sure.
I love both games tho, and for sure my next month will be all about FNV. However, I'm certain that next time I get urges, it will be FO3 that I return to. If only FO3 had the tech changes and gameplay changes that FNV has. Imagine hardcoe mode and drinking out of toilets underground in DC. That'd rule.